conda失败说没有写权限_使用conda安装vep

前面我们在进行突变注释的时候&＃xff0c;发现 VEP 安装非常麻烦&＃xff0c;原始安装方法会出现各种 perl 模块缺失的问题&＃xff0c;如果管理员权限&＃xff0c;倒是可以用 docker 安装。现实情况是&＃xff0c;大部分人是没有管理员权限的&＃xff0c;所以我推荐自己购买一个云服务器。今天&＃xff0c;给大家带来一种简便的 VEP 安装方法&＃xff0c;就是对新手非常友好的 conda&＃xff0c;从此不用再担心 perl 模块安装失败了。

参考&＃xff1a;https://bioconda.github.io/recipes/ensembl-vep/README.html

下载安装

conda 的安装方法就不再介绍了&＃xff0c;技能树已经发过非常多的教程了。我们直接安装 VEP &＃xff0c;为了不造成环境依赖相冲突&＃xff0c;可以新建一个小环境&＃xff0c;然后在小环境中安装 VEP

conda create -n vep
conda activate vep
conda install ensembl-vep


检查软件是否下载成功的最简单方法是调用帮助文档&＃xff1a;

$ vep --help
#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

Versions:
  ensembl              : 100.7e964b7
  ensembl-funcgen      : 100.f0c3948
  ensembl-io           : 100.f87ae4f
  ensembl-variation    : 100.1074e16
  ensembl-vep          : 100.1

Help: dev&＃64;ensembl.org , helpdesk&＃64;ensembl.org
Twitter: &＃64;ensembl

http://www.ensembl.org/info/docs/tools/vep/script/index.html

Usage:
./vep [--cache|--offline|--database] [arguments]

Basic options
&＃61;&＃61;&＃61;&＃61;&＃61;&＃61;&＃61;&＃61;&＃61;&＃61;&＃61;&＃61;&＃61;

--help                 Display this message and quit

-i | --input_file      Input file
-o | --output_file     Output file
--force_overwrite      Force overwriting of output file
--species [species]    Species to use [default: "human"]

--everything           Shortcut switch to turn on commonly used options. See web
                       documentation for details [default: off]                       
--fork [num_forks]     Use forking to improve script runtime

For full option documentation see:
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html


我下载的时候默认就是最新版&＃xff1a;ensembl-vep-100.(截止2020-05-25)&＃xff0c;如果之前安装过了旧版&＃xff0c;也可以用下面方法更新(不建议随便更新)&＃xff1a;

conda update ensembl-vep


不管是使用什么安装方法&＃xff0c;都需要下载数据库的基因组注释文件&＃xff0c;比如人类 GRCh38&＃xff0c;需要注意的是&＃xff0c;如果是用原始的安装方法(非conda)下载数据的命令是 INSTALL.pl &＃xff0c;而在这里已经改为了 vep_install。另一个需要注意的细节是&＃xff0c;数据库注释文件要与软件版本保持一致。不过数据库注释文件非常大&＃xff0c;光这个 GRCh38 版本的人类基因组注释文件就要 14 G&＃xff0c;还是压缩版本的。

mkdir ~/wes_cancer/data/vep
vep_install -a cf -s homo_sapiens -y GRCh38 -c ~/wes_cancer/data/vep –CONVERT
# 也可以自行下来解压&＃xff0c;比如&＃xff1a;
cd ~/wes_cancer/data/vep
curl -O ftp://ftp.ensembl.org/pub/release-100/variation/indexed_vep_cache/homo_sapiens_vep_100_GRCh38.tar.gz
tar -zxvf homo_sapiens_vep_100_GRCh38.tar.gz
# 解压后生成文件夹&＃xff0c;里面有大量的注释文件
ls homo_sapiens/100_GRCh38/ | head
1
10
11
12
13
14
15
16
17
18


官网建议&＃xff0c;注释文件要与软件版本号对应&＃xff0c;比如这里用的是 ensembl-vep-100&＃xff0c;注释信息包含了以下&＃xff1a;

注释

首先要理解参数&＃xff0c;看官网就好 http://asia.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_genomes&＃xff0c;这里用到了几个参数&＃xff1a;

一个 327 个位点的 vcf 文件运行时间约3分钟&＃xff0c;代码和结果如下&＃xff1a;

vep --cache   --everything  \
--species homo_sapiens      \
--cache                     \
--dir ~/wes_cancer/data/vep \
--clin_sig_allele 0         \
--af  --af_gnomad --af_exac \
--fasta ~/wes_cancer/data/Homo_sapiens_assembly38.fasta \
--stats_text --stats_file 7.annotation/vep/case1_biorep_A_techrep_vep_summary.html       \
-i 6.mutect/case1_biorep_A_techrep_filter.vcf           \
--vcf                       \
-o 7.annotation/vep/case1_biorep_A_techrep_vep_tmp.vcf   


$ less 7.annotation/vep/case1_biorep_A_techrep_vep_tmp.vcf | grep -v &＃39;##&＃39; | head -10
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  case1_biorep_A_techrep  case1_germline
chr1    6146376 .   G   T   .   PASS    CONTQ&＃61;93;DP&＃61;205;ECNT&＃61;1;GERMQ&＃61;93;MBQ&＃61;31,38;MFRL&＃61;146,210;MMQ&＃61;60,60;MPOS&＃61;29;NALOD&＃61;1.89;NLOD&＃61;22.56;POPAF&＃61;6.00;SEQQ&＃61;12;STRANDQ&＃61;6;TLOD&＃61;5.40;CSQ&＃61;T|missense_variant|MODERATE|CHD5|ENSG00000116254|Transcript|ENST00000262450|protein_coding|11/42||ENST00000262450.8:c.1638C>A|ENSP00000262450.3:p.Asn546Lys|1936|1638|546|N/K|aaC/aaA|rs1041067908||-1||SNV|HGNC|HGNC:16816|YES|NM_015557.3|1|P1|CCDS57.1|ENSP00000262450|Q8TDI0||UPI000006CD03||tolerated(0.06)|benign(0.353)|Gene3D:2.40.50.40&PROSITE_profiles:PS50013&PANTHER:PTHR45623&PANTHER:PTHR45623:SF6&SMART:SM00298&Superfamily:SSF54160||||||||||||||||||||3.978e-06|0|0|0|0|0|8.793e-06|0|0|8.793e-06|gnomAD_NFE||||||||,T|upstream_gene_variant|MODIFIER|CHD5|ENSG00000116254|Transcript|ENST00000462991|nonsense_mediated_decay||||||||||rs1041067908|2272|-1|cds_start_NF|SNV|HGNC|HGNC:16816|||1|||ENSP00000466706||K7EMY3|UPI0002841241||||||||||||||||||||||||3.978e-06|0|0|0|0|0|8.793e-06|0|0|8.793e-06|gnomAD_NFE||||||||,T|missense_variant&NMD_transcript_variant|MODERATE|CHD5|ENSG00000116254|Transcript|ENST00000496404|nonsense_mediated_decay|11/34||ENST00000496404.1:c.1638C>A|ENSP00000433676.1:p.Asn546Lys|1638|1638|546|N/K|aaC/aaA|rs1041067908||-1||SNV|HGNC|HGNC:16816|||2|||ENSP00000433676||F2Z2R5|UPI0000470971||tolerated(0.08)|possibly_damaging(0.828)|||||||||||||||||||||3.978e-06|0|0|0|0|0|8.793e-06|0|0|8.793e-06|gnomAD_NFE|||||||| GT:AD:AF:DP:F1R2:F2R1:SB    0/1:108,3:0.039:111:52,1:55,2:40,68,2,1 0/0:85,0:0.013:85:50,0:34,0:33,52,0,0
chr1    6461445 .   G   T   .   PASS    CONTQ&＃61;93;DP&＃61;22;ECNT&＃61;1;GERMQ&＃61;28;MBQ&＃61;25,39;MFRL&＃61;170,184;MMQ&＃61;60,60;MPOS&＃61;14;NALOD&＃61;1.05;NLOD&＃61;2.70;POPAF&＃61;6.00;SEQQ&＃61;8;STRANDQ&＃61;10;TLOD&＃61;6.33;CSQ&＃61;T|downstream_gene_variant|MODIFIER|PLEKHG5|ENSG00000171680|Transcript|ENST00000340850|protein_coding|||||||||||4647|-1||SNV|HGNC|HGNC:29105|||5|P3|CCDS79.1|ENSP00000344570|O94827||UPI000015F97E|1|||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|TNFRSF25|ENSG00000215788|Transcript|ENST00000348333|protein_coding|9/9||ENST00000348333.7:c.1108C>A|ENSP00000314451.3:p.Arg370Ser|1108|1108|370|R/S|Cgc/Agc|||-1||SNV|HGNC|HGNC:11910|||1||CCDS74.1|ENSP00000314451|Q93038||UPI000002B5C9||deleterious(0.02)|probably_damaging(0.923)|Gene3D:1.10.533.10&Prints:PR01972&PANTHER:PTHR47220||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|TNFRSF25|ENSG00000215788|Transcript|ENST00000351748|protein_coding|5/5||ENST00000351748.7:c.694C>A|ENSP00000326762.3:p.Arg232Ser|694|694|232|R/S|Cgc/Agc|||-1||SNV|HGNC|HGNC:11910|||1||CCDS75.1|ENSP00000326762|Q93038||UPI000002B5C8||deleterious(0.01)|possibly_damaging(0.569)|Gene3D:1.10.533.10&PANTHER:PTHR47220||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|TNFRSF25|ENSG00000215788|Transcript|ENST00000351959|protein_coding|9/9||ENST00000351959.9:c.1132C>A|ENSP00000337713.5:p.Arg378Ser|1200|1132|378|R/S|Cgc/Agc|||-1||SNV|HGNC|HGNC:11910|||1|A2|CCDS73.1|ENSP00000337713|Q93038||UPI000002B5CA||deleterious(0.02)|possibly_damaging(0.865)|Gene3D:1.10.533.10&Prints:PR01972&PANTHER:PTHR47220||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|TNFRSF25|ENSG00000215788|Transcript|ENST00000356876|protein_coding|10/10||ENST00000356876.7:c.1243C>A|ENSP00000349341.3:p.Arg415Ser|1331|1243|415|R/S|Cgc/Agc|||-1||SNV|HGNC|HGNC:11910|||1|A2|CCDS71.1|ENSP00000349341|Q93038||UPI000003597B||deleterious(0.03)|possibly_damaging(0.737)|Gene3D:1.10.533.10&PDB-ENSP_mappings:5yev.A&PDB-ENSP_mappings:5yev.B&PDB-ENSP_mappings:5yev.C&PDB-ENSP_mappings:5yev.D&PDB-ENSP_mappings:5ygp.A&PDB-ENSP_mappings:5ygp.B&PDB-ENSP_mappings:5ygp.C&PDB-ENSP_mappings:5ygp.D&PDB-ENSP_mappings:5ygs.A&PDB-ENSP_mappings:5ygs.B&PDB-ENSP_mappings:5ygs.C&PDB-ENSP_mappings:5ygs.D&Prints:PR01972&PANTHER:PTHR47220||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|PLEKHG5|ENSG00000171680|Transcript|ENST00000377748|protein_coding|||||||||||4647|-1||SNV|HGNC|HGNC:29105|||2|A2|CCDS41240.1|ENSP00000366977|O94827||UPI0000199544|1|||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|TNFRSF25|ENSG00000215788|Transcript|ENST00000377782|protein_coding|10/10||ENST00000377782.7:c.1270C>A|ENSP00000367013.3:p.Arg424Ser|1338|1270|424|R/S|Cgc/Agc|||-1||SNV|HGNC|HGNC:11910|YES||1|P4|CCDS72.1|ENSP00000367013|Q93038||UPI000002B5CB||deleterious(0.01)|probably_damaging(0.943)|Gene3D:1.10.533.10&Prints:PR01972&PANTHER:PTHR47220||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|PLEKHG5|ENSG00000171680|Transcript|ENST00000400913|protein_coding|||||||||||4647|-1||SNV|HGNC|HGNC:29105|||5|P3|CCDS79.1|ENSP00000383704|O94827||UPI000015F97E|1|||||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000414040|nonsense_mediated_decay|9/9||ENST00000414040.6:c.*530C>A||1187|||||||-1||SNV|HGNC|HGNC:11910|||1|||ENSP00000404274|Q93038||UPI000002B5C3||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ESPN|ENSG00000187017|Transcript|ENST00000416731|protein_coding|||||||||||1047|1||SNV|HGNC|HGNC:13281|||5|||ENSP00000399239||A0A0A0MSQ4|UPI0004E4CD17|1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ESPN|ENSG00000187017|Transcript|ENST00000434576|protein_coding|||||||||||78|1|cds_start_NF|SNV|HGNC|HGNC:13281|||3|||ENSP00000413621||H0Y7L4|UPI000059CF5B|1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000453260|retained_intron|||||||||||35|-1||SNV|HGNC|HGNC:11910|||2||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000453341|retained_intron|||||||||||2666|-1||SNV|HGNC|HGNC:11910|||1||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000461703|processed_transcript|||||||||||2091|-1||SNV|HGNC|HGNC:11910|||1||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ESPN|ENSG00000187017|Transcript|ENST00000461727|protein_coding|||||||||||1046|1||SNV|HGNC|HGNC:13281|||1|||ENSP00000465308|B1AK53||UPI000173A9EC|1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ESPN|ENSG00000187017|Transcript|ENST00000468561|processed_transcript|||||||||||78|1||SNV|HGNC|HGNC:13281|||2|||||||1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000469691|retained_intron|||||||||||549|-1||SNV|HGNC|HGNC:11910|||3||||||||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000473343|retained_intron|4/4||ENST00000473343.5:n.1297C>A||1297|||||||-1||SNV|HGNC|HGNC:11910|||2||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ESPN|ENSG00000187017|Transcript|ENST00000475228|protein_coding|||||||||||1393|1|cds_end_NF|SNV|HGNC|HGNC:13281|||5|||ENSP00000488721||A0A0J9YY76|UPI000D19029C|1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000475730|processed_transcript|||||||||||311|-1||SNV|HGNC|HGNC:11910|||3||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ESPN|ENSG00000187017|Transcript|ENST00000477679|protein_coding|||||||||||1040|1|cds_start_NF|SNV|HGNC|HGNC:13281|||2|||ENSP00000495669||A0A2R8YG57|UPI000D18D84A|1|||||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000480393|nonsense_mediated_decay|9/9||ENST00000480393.5:c.*582C>A||1412|||||||-1||SNV|HGNC|HGNC:11910|||1|||ENSP00000434129||A0A0C4DGF3|UPI000016099B||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000481401|protein_coding|||||||||||1192|-1|cds_end_NF|SNV|HGNC|HGNC:11910|||5|||ENSP00000465381||K7EJY9|UPI0002841278||||||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000485036|nonsense_mediated_decay|9/9||ENST00000485036.5:c.*530C>A||1432|||||||-1||SNV|HGNC|HGNC:11910|||1|||ENSP00000431554|Q93038||UPI000002B5CC||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|PLEKHG5|ENSG00000171680|Transcript|ENST00000489097|retained_intron|||||||||||4647|-1||SNV|HGNC|HGNC:29105|||2|||||||1|||||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000502588|nonsense_mediated_decay|7/7||ENST00000502588.5:c.*530C>A||941|||||||-1||SNV|HGNC|HGNC:11910|||1|||ENSP00000423121|Q93038||UPI000002B5C6||||||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000502730|nonsense_mediated_decay|5/5||ENST00000502730.5:c.*446C>A||827|||||||-1||SNV|HGNC|HGNC:11910|||1|||ENSP00000421976|Q93038||UPI000002B5C7||||||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000510563|nonsense_mediated_decay|8/8||ENST00000510563.5:c.*530C>A||1076|||||||-1||SNV|HGNC|HGNC:11910|||1|||ENSP00000424071|Q93038||UPI000002B5C5||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000513135|retained_intron|6/6||ENST00000513135.5:n.3189C>A||3189|||||||-1||SNV|HGNC|HGNC:11910|||5||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|TNFRSF25|ENSG00000215788|Transcript|ENST00000515145|retained_intron|||||||||||3122|-1||SNV|HGNC|HGNC:11910|||4||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|PLEKHG5|ENSG00000171680|Transcript|ENST00000535355|protein_coding|||||||||||4647|-1||SNV|HGNC|HGNC:29105|||2|A2|CCDS57968.1|ENSP00000441445|O94827||UPI000206539F|1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|PLEKHG5|ENSG00000171680|Transcript|ENST00000537245|protein_coding|||||||||||4647|-1||SNV|HGNC|HGNC:29105|YES||2|A2|CCDS57969.1|ENSP00000439625|O94827||UPI000206539E|1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ESPN|ENSG00000187017|Transcript|ENST00000633239|protein_coding|||||||||||519|1|cds_start_NF|SNV|HGNC|HGNC:13281|||5|||ENSP00000488071||A0A0J9YWQ8|UPI00064546C6|1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ESPN|ENSG00000187017|Transcript|ENST00000636330|protein_coding|||||||||||4774|1||SNV|HGNC|HGNC:13281|||5|A2||ENSP00000490186||A0A1B0GUN9|UPI0007E52ADA|1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ESPN|ENSG00000187017|Transcript|ENST00000636644|protein_coding|||||||||||4182|1|cds_end_NF|SNV|HGNC|HGNC:13281|||5|||ENSP00000490230||A0A1B0GUS9|UPI0007E52A58|1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ESPN|ENSG00000187017|Transcript|ENST00000645284|protein_coding|||||||||||501|1||SNV|HGNC|HGNC:13281|YES|NM_031475.3||P2|CCDS70.1|ENSP00000496593|B1AK53||UPI000013D2B6|1|||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|TNFRSF25|ENSG00000215788|Transcript|ENST00000647810|protein_coding|9/9||ENST00000647810.1:c.1111C>A|ENSP00000497258.1:p.Arg371Ser|1111|1111|371|R/S|Cgc/Agc|||-1|cds_start_NF|SNV|HGNC|HGNC:11910||||||ENSP00000497258||A0A3B3ISD9|UPI000E6F2B68||deleterious(0.02)|probably_damaging(0.99)|Gene3D:1.10.533.10&PANTHER:PTHR47220||||||||||||||||||||||||||||||||||||||  GT:AD:AF:DP:F1R2:F2R1:SB    0/1:6,2:0.298:8:3,2:3,0:6,0,2,0 0/0:10,0:0.083:10:3,0:7,0:9,1,0,0
chr1    31756671    .   C   A   .   PASS    CONTQ&＃61;93;DP&＃61;196;ECNT&＃61;1;GERMQ&＃61;93;MBQ&＃61;36,32;MFRL&＃61;139,128;MMQ&＃61;60,60;MPOS&＃61;12;NALOD&＃61;1.54;NLOD&＃61;9.93;POPAF&＃61;6.00;SEQQ&＃61;93;STRANDQ&＃61;4;TLOD&＃61;19.01;CSQ&＃61;A|missense_variant|MODERATE|ADGRB2|ENSG00000121753|Transcript|ENST00000373655|protein_coding|4/33||ENST00000373655.6:c.166G>T|ENSP00000362759.2:p.Asp56Tyr|508|166|56|D/Y|Gac/Tac|||-1||SNV|HGNC|HGNC:944|YES||1|P4|CCDS72747.1|ENSP00000362759|O60241||UPI000046FEC7||deleterious(0.01)|probably_damaging(0.953)|||||||||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|ADGRB2|ENSG00000121753|Transcript|ENST00000373658|protein_coding|4/33||ENST00000373658.7:c.166G>T|ENSP00000362762.3:p.Asp56Tyr|520|166|56|D/Y|Gac/Tac|||-1||SNV|HGNC|HGNC:944|||5|A2||ENSP00000362762|O60241||UPI0000E2A42F||deleterious(0.01)|possibly_damaging(0.862)|||||||||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|ADGRB2|ENSG00000121753|Transcript|ENST00000398538|protein_coding|1/29||ENST00000398538.5:c.130G>T|ENSP00000381548.1:p.Asp44Tyr|131|130|44|D/Y|Gac/Tac|||-1||SNV|HGNC|HGNC:944|||5|A2||ENSP00000381548||A2A3C2|UPI0000EDA27D||deleterious(0.01)|probably_damaging(0.921)|||||||||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|ADGRB2|ENSG00000121753|Transcript|ENST00000398542|protein_coding|2/28||ENST00000398542.5:c.130G>T|ENSP00000381550.1:p.Asp44Tyr|602|130|44|D/Y|Gac/Tac|||-1||SNV|HGNC|HGNC:944|||5|||ENSP00000381550||A2A3C1|UPI0000EDA27C||deleterious(0.01)|possibly_damaging(0.887)|||||||||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|ADGRB2|ENSG00000121753|Transcript|ENST00000398547|protein_coding|2/29||ENST00000398547.5:c.130G>T|ENSP00000381555.1:p.Asp44Tyr|184|130|44|D/Y|Gac/Tac|||-1||SNV|HGNC|HGNC:944|||5|A2||ENSP00000381555||A2A3C3|UPI0000EDA27E||deleterious(0.01)|possibly_damaging(0.887)|||||||||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|ADGRB2|ENSG00000121753|Transcript|ENST00000398556|protein_coding|2/29||ENST00000398556.7:c.175G>T|ENSP00000381564.3:p.Asp59Tyr|248|175|59|D/Y|Gac/Tac|||-1||SNV|HGNC|HGNC:944|||5|A2||ENSP00000381564||A2A3C6|UPI0000EDA282||deleterious(0.01)|possibly_damaging(0.887)|||||||||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|ADGRB2|ENSG00000121753|Transcript|ENST00000420125|protein_coding|1/14||ENST00000420125.5:c.145G>T|ENSP00000410921.1:p.Asp49Tyr|145|145|49|D/Y|Gac/Tac|||-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:944|||2|||ENSP00000410921||A2A3C4|UPI0000EDA27F||deleterious(0)|possibly_damaging(0.887)|||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ADGRB2|ENSG00000121753|Transcript|ENST00000436464|protein_coding|||||||||||546|-1|cds_end_NF|SNV|HGNC|HGNC:944|||4|||ENSP00000414758|||UPI0000055EF8||||||||||||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|ADGRB2|ENSG00000121753|Transcript|ENST00000527361|protein_coding|2/30||ENST00000527361.5:c.166G>T|ENSP00000435397.1:p.Asp56Tyr|204|166|56|D/Y|Gac/Tac|||-1||SNV|HGNC|HGNC:944|||1|A2|CCDS72746.1|ENSP00000435397|O60241||UPI00019B21E0||deleterious(0.01)|probably_damaging(0.977)|||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ADGRB2|ENSG00000121753|Transcript|ENST00000530134|processed_transcript|||||||||||407|-1||SNV|HGNC|HGNC:944|||2||||||||||||||||||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|ADGRB2|ENSG00000121753|Transcript|ENST00000533175|protein_coding|2/6||ENST00000533175.1:c.268G>T|ENSP00000437219.1:p.Asp90Tyr|359|268|90|D/Y|Gac/Tac|||-1|cds_end_NF|SNV|HGNC|HGNC:944|||1|||ENSP00000437219||E9PND1|UPI0001891DD1||deleterious(0)|probably_damaging(0.987)|||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|MIR4254|ENSG00000266580|Transcript|ENST00000581063|miRNA|||||||||||1989|-1||SNV|HGNC|HGNC:38193|YES||||||||||||||||||||||||||||||||||||||||||||||||||    GT:AD:AF:DP:F1R2:F2R1:SB    0/1:138,10:0.076:148:75,6:61,4:57,81,1,9    0/0:38,0:0.028:38:12,0:26,0:14,24,0,0
chr1    32037007    .   G   T   .   PASS    CONTQ&＃61;93;DP&＃61;374;ECNT&＃61;1;GERMQ&＃61;93;MBQ&＃61;37,33;MFRL&＃61;151,127;MMQ&＃61;60,60;MPOS&＃61;13;NALOD&＃61;2.10;NLOD&＃61;37.23;POPAF&＃61;6.00;SEQQ&＃61;9;STRANDQ&＃61;8;TLOD&＃61;4.80;CSQ&＃61;T|non_coding_transcript_exon_variant|MODIFIER|KHDRBS1|ENSG00000121774|Transcript|ENST00000307714|processed_transcript|5/9||ENST00000307714.12:n.939G>T||939|||||||1||SNV|HGNC|HGNC:18116|||1||||||||||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|KHDRBS1|ENSG00000121774|Transcript|ENST00000327300|protein_coding|5/9||ENST00000327300.12:c.869G>T|ENSP00000313829.7:p.Gly290Val|997|869|290|G/V|gGc/gTc|||1||SNV|HGNC|HGNC:18116|YES|NM_006559.3|1|P1|CCDS350.1|ENSP00000313829|Q07666||UPI0000073DA7||deleterious(0.03)|probably_damaging(0.999)|PANTHER:PTHR11208&PANTHER:PTHR11208:SF30&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|KHDRBS1|ENSG00000121774|Transcript|ENST00000484270|processed_transcript|5/11||ENST00000484270.2:n.683G>T||683|||||||1||SNV|HGNC|HGNC:18116|||5||||||||||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|KHDRBS1|ENSG00000121774|Transcript|ENST00000492989|protein_coding|4/8||ENST00000492989.1:c.752G>T|ENSP00000417731.1:p.Gly251Val|752|752|251|G/V|gGc/gTc|||1||SNV|HGNC|HGNC:18116|||1||CCDS60067.1|ENSP00000417731|Q07666||UPI0000071FE8||deleterious(0.01)|probably_damaging(1)|PANTHER:PTHR11208&PANTHER:PTHR11208:SF30&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg||||||||||||||||||||||||||||||||||||||   GT:AD:AF:DP:F1R2:F2R1:SB    0/1:213,4:0.025:217:105,0:105,4:55,158,1,3  0/0:135,0:7.839e-03:135:67,0:66,0:42,93,0,0
chr1    42842803    .   G   T   .   PASS    CONTQ&＃61;93;DP&＃61;238;ECNT&＃61;1;GERMQ&＃61;93;MBQ&＃61;39,32;MFRL&＃61;175,195;MMQ&＃61;60,60;MPOS&＃61;17;NALOD&＃61;1.72;NLOD&＃61;13.85;POPAF&＃61;6.00;SEQQ&＃61;10;STRANDQ&＃61;2;TLOD&＃61;4.99;CSQ&＃61;T|non_coding_transcript_exon_variant|MODIFIER|ERMAP|ENSG00000164010|Transcript|ENST00000328249|retained_intron|9/9||ENST00000328249.3:n.1767G>T||1767|||||||1||SNV|HGNC|HGNC:15743|||1|||||||1|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|ZNF691|ENSG00000164011|Transcript|ENST00000372502|protein_coding|||||||||||3770|1||SNV|HGNC|HGNC:28028|YES||2|A2|CCDS55595.1|ENSP00000361580|Q5VV52||UPI0000EE2FE8||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|ZNF691|ENSG00000164011|Transcript|ENST00000372504|protein_coding|||||||||||3834|1||SNV|HGNC|HGNC:28028|||5|A2||ENSP00000361582||Q5VV50|UPI0000458A28||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|ZNF691|ENSG00000164011|Transcript|ENST00000372506|protein_coding|||||||||||3825|1||SNV|HGNC|HGNC:28028|||2|P3|CCDS476.1|ENSP00000361584|Q5VV52||UPI00000437B0||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|ZNF691|ENSG00000164011|Transcript|ENST00000372507|protein_coding|||||||||||3823|1||SNV|HGNC|HGNC:28028|||3|P3|CCDS476.1|ENSP00000361585|Q5VV52||UPI00000437B0||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|ZNF691|ENSG00000164011|Transcript|ENST00000372508|protein_coding|||||||||||3806|1||SNV|HGNC|HGNC:28028|||1|P3|CCDS476.1|ENSP00000361586|Q5VV52||UPI00000437B0||||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|ERMAP|ENSG00000164010|Transcript|ENST00000372514|protein_coding|11/11||ENST00000372514.7:c.999G>T|ENSP00000361592.3:p.Gln333His|1183|999|333|Q/H|caG/caT|||1||SNV|HGNC|HGNC:15743|||1|P1|CCDS475.1|ENSP00000361592|Q96PL5|A0A1C9HIH9|UPI000007000D|1|tolerated(0.06)|benign(0.09)|Gene3D:2.60.120.920&Pfam:PF00622&PROSITE_profiles:PS50188&PANTHER:PTHR24100&PANTHER:PTHR24100:SF46&SMART:SM00449&Superfamily:SSF49899&CDD:cd15813||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|ERMAP|ENSG00000164010|Transcript|ENST00000372517|protein_coding|12/12||ENST00000372517.8:c.999G>T|ENSP00000361595.2:p.Gln333His|1252|999|333|Q/H|caG/caT|||1||SNV|HGNC|HGNC:15743|YES|NM_001017922.2|1|P1|CCDS475.1|ENSP00000361595|Q96PL5|A0A1C9HIH9|UPI000007000D|1|tolerated(0.06)|benign(0.09)|PROSITE_profiles:PS50188&CDD:cd15813&PANTHER:PTHR24100&PANTHER:PTHR24100:SF46&Pfam:PF00622&Gene3D:2.60.120.920&SMART:SM00449&Superfamily:SSF49899||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|AL512353.1|ENSG00000228192|Transcript|ENST00000414798|lncRNA||1/1|ENST00000414798.1:n.63&＃43;3557C>A|||||||||-1||SNV|Clone_based_ensembl_gene||||3||||||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|AL512353.1|ENSG00000228192|Transcript|ENST00000416809|lncRNA||1/2|ENST00000416809.2:n.106&＃43;3454C>A|||||||||-1||SNV|Clone_based_ensembl_gene||||3||||||||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|AL512353.1|ENSG00000228192|Transcript|ENST00000425076|lncRNA|4/5||ENST00000425076.1:n.392C>A||392|||||||-1||SNV|Clone_based_ensembl_gene||||3||||||||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|AL512353.1|ENSG00000228192|Transcript|ENST00000444563|lncRNA|4/5||ENST00000444563.5:n.466C>A||466|||||||-1||SNV|Clone_based_ensembl_gene||||2||||||||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|ERMAP|ENSG00000164010|Transcript|ENST00000487556|processed_transcript|11/11||ENST00000487556.6:n.1013G>T||1013|||||||1||SNV|HGNC|HGNC:15743|||5|||||||1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ERMAP|ENSG00000164010|Transcript|ENST00000642150|retained_intron|||||||||||3090|1||SNV|HGNC|HGNC:15743||||||||||1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ERMAP|ENSG00000164010|Transcript|ENST00000647120|processed_transcript|||||||||||275|1||SNV|HGNC|HGNC:15743||||||||||1|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|ZNF691|ENSG00000164011|Transcript|ENST00000651192|protein_coding|||||||||||3810|1||SNV|HGNC|HGNC:28028||NM_001242739.2||A2|CCDS55595.1|ENSP00000498913|Q5VV52||UPI0000EE2FE8||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|AL512353.1|ENSG00000228192|Transcript|ENST00000659750|lncRNA|4/5||ENST00000659750.1:n.493C>A||493|||||||-1||SNV|Clone_based_ensembl_gene||YES|||||||||||||||||||||||||||||||||||||||||||||||||| GT:AD:AF:DP:F1R2:F2R1:SB    0/1:171,4:0.029:175:96,2:74,2:60,111,3,1    0/0:47,0:0.019:47:26,0:21,0:13,34,0,0
chr1    43569766    .   C   G   .   PASS    CONTQ&＃61;93;DP&＃61;132;ECNT&＃61;1;GERMQ&＃61;93;MBQ&＃61;39,41;MFRL&＃61;154,172;MMQ&＃61;60,60;MPOS&＃61;19;NALOD&＃61;1.48;NLOD&＃61;8.43;POPAF&＃61;6.00;SEQQ&＃61;93;STRANDQ&＃61;16;TLOD&＃61;37.99;CSQ&＃61;G|missense_variant|MODERATE|PTPRF|ENSG00000142949|Transcript|ENST00000359947|protein_coding|6/34||ENST00000359947.9:c.556C>G|ENSP00000353030.4:p.Gln186Glu|889|556|186|Q/E|Cag/Gag|||1||SNV|HGNC|HGNC:9670|YES|NM_002840.5|1|P4|CCDS489.2|ENSP00000353030|P10586||UPI0000470154|1|tolerated(0.2)|probably_damaging(0.986)|Gene3D:2.60.40.10&PDB-ENSP_mappings:2yd5.A&PDB-ENSP_mappings:2yd8.A&Pfam:PF07679&PROSITE_profiles:PS50835&PANTHER:PTHR19134&PANTHER:PTHR19134:SF203&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726&CDD:cd05738||||||||||||||||||||||||||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|PTPRF|ENSG00000142949|Transcript|ENST00000372405|processed_transcript|5/6||ENST00000372405.1:n.681C>G||681|||||||1||SNV|HGNC|HGNC:9670|||1|||||||1|||||||||||||||||||||||||||||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|PTPRF|ENSG00000142949|Transcript|ENST00000436724|processed_transcript|6/8||ENST00000436724.5:n.869C>G||869|||||||1||SNV|HGNC|HGNC:9670|||1|||||||1|||||||||||||||||||||||||||||||||||||||||,G|missense_variant|MODERATE|PTPRF|ENSG00000142949|Transcript|ENST00000437607|protein_coding|4/6||ENST00000437607.1:c.556C>G|ENSP00000413306.1:p.Gln186Glu|556|556|186|Q/E|Cag/Gag|||1|cds_end_NF|SNV|HGNC|HGNC:9670|||1|||ENSP00000413306||A2A437|UPI0000EDA28B|1|deleterious(0.01)|possibly_damaging(0.784)|PROSITE_profiles:PS50835&CDD:cd05738&PANTHER:PTHR13817:SF68&PANTHER:PTHR13817&Pfam:PF07679&Gene3D:2.60.40.10&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726||||||||||||||||||||||||||||||||||||||,G|missense_variant|MODERATE|PTPRF|ENSG00000142949|Transcript|ENST00000438120|protein_coding|6/33||ENST00000438120.5:c.556C>G|ENSP00000398822.1:p.Gln186Glu|882|556|186|Q/E|Cag/Gag|||1||SNV|HGNC|HGNC:9670|||1|A1|CCDS490.2|ENSP00000398822|P10586||UPI0000470155|1|tolerated(0.2)|benign(0.425)|CDD:cd05738&Pfam:PF07679&Gene3D:2.60.40.10&SMART:SM00409&SMART:SM00408&Superfamily:SSF48726&PROSITE_profiles:PS50835&PANTHER:PTHR19134:SF203&PANTHER:PTHR19134||||||||||||||||||||||||||||||||||||||,G|missense_variant|MODERATE|PTPRF|ENSG00000142949|Transcript|ENST00000617451|protein_coding|6/8||ENST00000617451.4:c.556C>G|ENSP00000483557.1:p.Gln186Glu|896|556|186|Q/E|Cag/Gag|||1||SNV|HGNC|HGNC:9670|||5|||ENSP00000483557||A2A437|UPI0000EDA28B|1|deleterious(0.01)|possibly_damaging(0.784)|Gene3D:2.60.40.10&Pfam:PF07679&PROSITE_profiles:PS50835&PANTHER:PTHR13817&PANTHER:PTHR13817:SF68&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726&CDD:cd05738||||||||||||||||||||||||||||||||||||||   GT:AD:AF:DP:F1R2:F2R1:SB    0/1:75,13:0.158:88:35,9:39,4:17,58,1,12 0/0:31,0:0.032:31:13,0:18,0:8,23,0,0
chr1    43683792    .   G   T   .   PASS    CONTQ&＃61;93;DP&＃61;295;ECNT&＃61;1;GERMQ&＃61;93;MBQ&＃61;37,33;MFRL&＃61;148,184;MMQ&＃61;60,60;MPOS&＃61;21;NALOD&＃61;1.87;NLOD&＃61;21.67;POPAF&＃61;6.00;SEQQ&＃61;12;STRANDQ&＃61;9;TLOD&＃61;5.15;CSQ&＃61;T|missense_variant|MODERATE|KDM4A|ENSG00000066135|Transcript|ENST00000372396|protein_coding|12/22||ENST00000372396.4:c.1843G>T|ENSP00000361473.3:p.Val615Phe|1986|1843|615|V/F|Gtc/Ttc|||1||SNV|HGNC|HGNC:22978|YES|NM_014663.3|1|P1|CCDS491.1|ENSP00000361473|O75164||UPI000013D35A||tolerated(0.18)|benign(0.014)|PANTHER:PTHR10694:SF51&PANTHER:PTHR10694||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|AL451062.4|ENSG00000284989|Transcript|ENST00000645057|nonsense_mediated_decay|6/26||ENST00000645057.1:c.*81G>T||875|||||||1||SNV|Clone_based_ensembl_gene||YES|||P1||ENSP00000494063||A0A2R8Y4U1|UPI000D197852||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|KDM4A-AS1|ENSG00000236200|Transcript|ENST00000663424|lncRNA|||||||||||1331|-1||SNV|HGNC|HGNC:40528|||||||||||||||||||||||||||||||||||||||||||||||||||   GT:AD:AF:DP:F1R2:F2R1:SB 0/1:191,4:0.027:195:98,3:92,1:56,135,2,2    0/0:84,0:0.013:84:42,0:42,0:24,60,0,0
chr1    61856152    .   G   T   .   PASS    CONTQ&＃61;93;DP&＃61;426;ECNT&＃61;1;GERMQ&＃61;93;MBQ&＃61;38,33;MFRL&＃61;149,185;MMQ&＃61;60,60;MPOS&＃61;22;NALOD&＃61;2.06;NLOD&＃61;33.41;POPAF&＃61;6.00;SEQQ&＃61;7;STRANDQ&＃61;9;TLOD&＃61;4.58;CSQ&＃61;T|missense_variant|MODERATE|PATJ|ENSG00000132849|Transcript|ENST00000316485|protein_coding|18/26||ENST00000316485.11:c.2235G>T|ENSP00000326199.7:p.Leu745Phe|2349|2235|745|L/F|ttG/ttT|||1||SNV|HGNC|HGNC:28881|||5|||ENSP00000326199||A0A0X1KG69|UPI00071AFB10||deleterious(0.01)|probably_damaging(0.982)|Gene3D:2.30.42.10&Pfam:PF00595&PROSITE_profiles:PS50106&PANTHER:PTHR19964&PANTHER:PTHR19964:SF11&SMART:SM00228&Superfamily:SSF50156&CDD:cd00992||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|PATJ|ENSG00000132849|Transcript|ENST00000371158|protein_coding|18/43||ENST00000371158.6:c.2235G>T|ENSP00000360200.2:p.Leu745Phe|2349|2235|745|L/F|ttG/ttT|||1||SNV|HGNC|HGNC:28881|||5||CCDS617.2|ENSP00000360200|Q8NI35||UPI0000204487||deleterious(0.01)|probably_damaging(0.981)|Gene3D:2.30.42.10&PDB-ENSP_mappings:2d92.A&Pfam:PF00595&PROSITE_profiles:PS50106&PANTHER:PTHR19964&PANTHER:PTHR19964:SF11&SMART:SM00228&Superfamily:SSF50156&CDD:cd00992||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|RNU6-1177P|ENSG00000212360|Transcript|ENST00000391058|snRNA|||||||||||3550|1||SNV|HGNC|HGNC:48140|YES||||||||||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|PATJ|ENSG00000132849|Transcript|ENST00000459752|retained_intron|18/34||ENST00000459752.5:n.2349G>T||2349|||||||1||SNV|HGNC|HGNC:28881|||1||||||||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|PATJ|ENSG00000132849|Transcript|ENST00000484562|retained_intron|18/35||ENST00000484562.5:n.2349G>T||2349|||||||1||SNV|HGNC|HGNC:28881|||1||||||||||||||||||||||||||||||||||||||||||||||||,T|missense_variant&NMD_transcript_variant|MODERATE|PATJ|ENSG00000132849|Transcript|ENST00000484937|nonsense_mediated_decay|6/33||ENST00000484937.5:c.612G>T|ENSP00000433669.1:p.Leu204Phe|624|612|204|L/F|ttG/ttT|||1||SNV|HGNC|HGNC:28881|||5|||ENSP00000433669|Q8NI35||UPI0000458A6F||deleterious(0.01)|probably_damaging(0.954)|||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|PATJ|ENSG00000132849|Transcript|ENST00000613764|protein_coding|18/29||ENST00000613764.4:c.2235G>T|ENSP00000479041.1:p.Leu745Phe|2332|2235|745|L/F|ttG/ttT|||1||SNV|HGNC|HGNC:28881|||5|||ENSP00000479041||A0A087WUZ6|UPI0004E4CA1E||deleterious(0)|probably_damaging(0.982)|Gene3D:2.30.42.10&Pfam:PF00595&PROSITE_profiles:PS50106&PANTHER:PTHR19964&PANTHER:PTHR19964:SF11&SMART:SM00228&Superfamily:SSF50156&CDD:cd00992||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|PATJ|ENSG00000132849|Transcript|ENST00000635023|nonsense_mediated_decay|19/36||ENST00000635023.1:c.*203G>T||2301|||||||1||SNV|HGNC|HGNC:28881|||5|||ENSP00000489335||A0A0U1RR46|UPI000719A1BD||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|PATJ|ENSG00000132849|Transcript|ENST00000635214|retained_intron|18/36||ENST00000635214.1:n.2349G>T||2349|||||||1||SNV|HGNC|HGNC:28881|||1||||||||||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|PATJ|ENSG00000132849|Transcript|ENST00000642238|protein_coding|18/44||ENST00000642238.1:c.2235G>T|ENSP00000494277.1:p.Leu745Phe|2420|2235|745|L/F|ttG/ttT|||1||SNV|HGNC|HGNC:28881|YES|||P1|CCDS85980.1|ENSP00000494277||A0A2R8Y549|UPI0000204496||deleterious(0.01)|probably_damaging(0.945)|Gene3D:2.30.42.10&Pfam:PF00595&PROSITE_profiles:PS50106&PANTHER:PTHR19964&PANTHER:PTHR19964:SF11&SMART:SM00228&Superfamily:SSF50156&CDD:cd00992||||||||||||||||||||||||||||||||||||||  GT:AD:AF:DP:F1R2:F2R1:SB    0/1:277,4:0.019:281:129,4:146,0:128,149,2,2  0/0:127,0:8.719e-03:127:53,0:74,0:59,68,0,0
chr1    65592818    .   G   T   .   PASS    CONTQ&＃61;93;DP&＃61;329;ECNT&＃61;1;GERMQ&＃61;93;MBQ&＃61;40,33;MFRL&＃61;163,200;MMQ&＃61;60,60;MPOS&＃61;13;NALOD&＃61;1.88;NLOD&＃61;21.37;POPAF&＃61;6.00;SEQQ&＃61;6;STRANDQ&＃61;8;TLOD&＃61;4.42;CSQ&＃61;T|missense_variant|MODERATE|LEPR|ENSG00000116678|Transcript|ENST00000344610|protein_coding|5/19||ENST00000344610.12:c.656G>T|ENSP00000340884.8:p.Gly219Val|806|656|219|G/V|gGa/gTa|||1||SNV|HGNC|HGNC:6554|||1||CCDS55604.1|ENSP00000340884|P48357||UPI000002AD2C|1|tolerated(0.4)|benign(0.052)|Gene3D:2.60.40.10&Pfam:PF18589&PANTHER:PTHR23036&PANTHER:PTHR23036:SF109||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|LEPR|ENSG00000116678|Transcript|ENST00000349533|protein_coding|6/20||ENST00000349533.10:c.656G>T|ENSP00000330393.6:p.Gly219Val|841|656|219|G/V|gGa/gTa|||1||SNV|HGNC|HGNC:6554|YES||1|P3|CCDS631.1|ENSP00000330393|P48357||UPI000014C37B|1|tolerated(1)|benign(0.015)|PANTHER:PTHR23036&PANTHER:PTHR23036:SF109&Gene3D:2.60.40.10&Pfam:PF18589||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|LEPR|ENSG00000116678|Transcript|ENST00000371058|protein_coding|4/18||ENST00000371058.1:c.656G>T|ENSP00000360097.1:p.Gly219Val|676|656|219|G/V|gGa/gTa|||1||SNV|HGNC|HGNC:6554|||5||CCDS55604.1|ENSP00000360097|P48357||UPI000002AD2C|1|tolerated(0.4)|benign(0.052)|PANTHER:PTHR23036:SF109&PANTHER:PTHR23036&Pfam:PF18589&Gene3D:2.60.40.10||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|LEPR|ENSG00000116678|Transcript|ENST00000371059|protein_coding|6/20||ENST00000371059.7:c.656G>T|ENSP00000360098.3:p.Gly219Val|841|656|219|G/V|gGa/gTa|||1||SNV|HGNC|HGNC:6554|||1||CCDS30741.1|ENSP00000360098|P48357||UPI000002AD2B|1|tolerated(0.33)|benign(0.023)|PANTHER:PTHR23036&PANTHER:PTHR23036:SF109&Pfam:PF18589&Gene3D:2.60.40.10||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|LEPR|ENSG00000116678|Transcript|ENST00000371060|protein_coding|6/20||ENST00000371060.7:c.656G>T|ENSP00000360099.3:p.Gly219Val|841|656|219|G/V|gGa/gTa|||1||SNV|HGNC|HGNC:6554|||1|A1|CCDS30740.1|ENSP00000360099|P48357||UPI000002AD2A|1|tolerated(0.41)|benign(0.034)|PANTHER:PTHR23036:SF109&PANTHER:PTHR23036&Pfam:PF18589&Gene3D:2.60.40.10||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|LEPR|ENSG00000116678|Transcript|ENST00000462765|processed_transcript|5/13||ENST00000462765.5:n.806G>T||806|||||||1||SNV|HGNC|HGNC:6554|||1|||||||1|||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|LEPR|ENSG00000116678|Transcript|ENST00000616738|protein_coding|5/19||ENST00000616738.4:c.656G>T|ENSP00000483390.1:p.Gly219Val|806|656|219|G/V|gGa/gTa|||1||SNV|HGNC|HGNC:6554|||1|A1|CCDS30740.1|ENSP00000483390|P48357||UPI000002AD2A|1|tolerated(0.41)|benign(0.034)|Gene3D:2.60.40.10&Pfam:PF18589&PANTHER:PTHR23036&PANTHER:PTHR23036:SF109||||||||||||||||||||||||||||||||||||||  GT:AD:AF:DP:F1R2:F2R1:SB    0/1:228,4:0.022:232:103,3:124,1:63,165,1,3  0/0:81,0:0.013:81:43,0:38,0:27,54,0,0


过滤

参考&＃xff1a;http://asia.ensembl.org/info/docs/tools/vep/script/vep_filter.html

过滤的方法有很多&＃xff0c;具体可以看上面的链接&＃xff0c;比如使用硬过滤&＃xff0c;直接过滤掉 AF <0.005 的位点

filter_vep -i 7.annotation/vep/case1_biorep_A_techrep_vep_tmp.vcf   --format vcf --filter "AF  -o 7.annotation/vep/case1_biorep_A_techrep_vep_filtered.vcf

网页版

如果连conda 安装都不会&＃xff0c;那也可以使用 VEP 网页版工具&＃xff1a;https://asia.ensembl.org/Homo_sapiens/Tools/VEP?db&＃61;core;expand_form&＃61;true;tl&＃61;FLl7RenUpSMXNLQv-6242040&＃xff0c;直接上传 vcf 文件即可注释

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