SnpEff: Mutation Site Annotation
Reference tutorial: https://www.jianshu.com/p/ad1ab3d7fcd0
SnpEff download link: http://snpeff.sourceforge.net/download.html
Download and Install Software
$ wget -c http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip
$ unzip snpEff_latest_core.zip
Check the installation status:
(wes) root@1100150:~/wes_cancer/biosoft# ll
total 607405
drwxr-xr-x 6 root root 9 Jun 27 01:04 ./
drwxr-xr-x 5 root root 5 Jun 18 08:37 ../
drwxr-xr-x 4 1002 jmzeng 19 Jun 19 11:29 annovar/
-rw-r--r-- 1 root root 141660305 Jun 9 18:46 annovar.latest.tar.gz
drwxrwxr-x 4 root root 7 Nov 24 2017 clinEff/
drwxr-xr-x 4 root root 12 Apr 23 19:10 gatk-4.1.7.0/
-rw-r--r-- 1 root root 410761523 Apr 23 23:11 gatk-4.1.7.0.zip
drwxrwxr-x 5 root root 8 Nov 24 2017 snpEff/
-rw-r--r-- 1 root root 69708122 Nov 24 2017 snpEff_latest_core.zip
(wes) root@1100150:~/wes_cancer/biosoft# ll snpEff/
total 39139
drwxrwxr-x 5 root root 8 Nov 24 2017 ./
drwxr-xr-x 6 root root 9 Jun 27 01:04 ../
-rw-rw-r-- 1 root root 18832860 Nov 24 2017 SnpSift.jar
drwxrwxr-x 2 root root 33 Nov 24 2017 examples/
drwxrwxr-x 3 root root 13 Nov 24 2017 galaxy/
drwxrwxr-x 3 root root 56 Nov 24 2017 scripts/
-rw-rw-r-- 1 root root 8196208 Nov 24 2017 snpEff.config
-rw-rw-r-- 1 root root 21277580 Nov 24 2017 snpEff.jar
(wes) root@1100150:~/wes_cancer/biosoft# cd snpEff/
(wes) root@1100150:~/wes_cancer/biosoft/snpEff# ll
total 39139
drwxrwxr-x 5 root root 8 Nov 24 2017 ./
drwxr-xr-x 6 root root 9 Jun 27 01:04 ../
-rw-rw-r-- 1 root root 18832860 Nov 24 2017 SnpSift.jar
drwxrwxr-x 2 root root 33 Nov 24 2017 examples/
drwxrwxr-x 3 root root 13 Nov 24 2017 galaxy/
drwxrwxr-x 3 root root 56 Nov 24 2017 scripts/
-rw-rw-r-- 1 root root 8196208 Nov 24 2017 snpEff.config
-rw-rw-r-- 1 root root 21277580 Nov 24 2017 snpEff.jar
Download Necessary Database Files
(wes) root@1100150:~/wes_cancer/biosoft/snpEff# java -jar snpEff.jar databases > snpEff.databases.list.txt
(wes) root@1100150:~/wes_cancer/biosoft/snpEff# head snpEff.databases.list.txt
Genome Organism Status Bundle Database download link
------ -------- ------ ------ ----------------------
129S1_SvImJ_v1.86 Mus_musculus_129s1svimj http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_129S1_SvImJ_v1.86.zip
AKR_J_v1.86 Mus_musculus_akrj http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_AKR_J_v1.86.zip
A_J_v1.86 Mus_musculus_aj http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_A_J_v1.86.zip
Abiotrophia_defectiva_atcc_49176 Abiotrophia_defectiva_atcc_49176 ENSEMBL_BFMPP_32_1 http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_ENSEMBL_BFMPP_32_1.zip
Acanthamoeba_castellanii_str_neff Acanthamoeba_castellanii_str_neff ENSEMBL_BFMPP_32_1 http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_ENSEMBL_BFMPP_32_1.zip
Acaryochloris_marina_mbic11017 Acaryochloris_marina_mbic11017 ENSEMBL_BFMPP_32_1 http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_ENSEMBL_BFMPP_32_1.zip
Acetivibrio_ethanolgignens Acetivibrio_ethanolgignens ENSEMBL_BFMPP_32_1 http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_ENSEMBL_BFMPP_32_1.zip
Acetobacter_aceti_1023 Acetobacter_aceti_1023 ENSEMBL_BFMPP_32_1 http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_ENSEMBL_BFMPP_32_1.zip
(wes) root@1100150:~/wes_cancer/biosoft/snpEff# grep -i 'Homo_sapiens' snpEff.databases.list.txt |cut -f1
GRCh37.75
GRCh38.86
hg19
hg19kg
hg38
hg38kg
testHg19ChrM
(wes) root@1100150:~/wes_cancer/biosoft/snpEff# java -jar snpEff.jar download GRCh38.86
(wes) root@1100150:~/wes_cancer/biosoft/snpEff# ll
total 40440
drwxrwxr-x 6 root root 10 Jun 27 01:10 ./
drwxr-xr-x 6 root root 9 Jun 27 01:04 ../
-rw-rw-r-- 1 root root 18832860 Nov 24 2017 SnpSift.jar
drwxr-xr-x 3 root root 3 Jun 27 01:10 data/
drwxrwxr-x 2 root root 33 Nov 24 2017 examples/
drwxrwxr-x 3 root root 13 Nov 24 2017 galaxy/
drwxrwxr-x 3 root root 56 Nov 24 2017 scripts/
-rw-rw-r-- 1 root root 8196208 Nov 24 2017 snpEff.config
-rw-r--r-- 1 root root 11328178 Jun 27 01:06 snpEff.databases.list.txt
-rw-rw-r-- 1 root root 21277580 Nov 24 2017 snpEff.jar
The line drwxr-xr-x 3 root root 3 Jun 27 01:10 data/ indicates the latest version of the human reference genome database file I downloaded.
SNP Site Annotation
Locate the filtered VCF file obtained earlier and annotate it using SnpEff.
(wes) root@1100150:~/wes_cancer/biosoft/snpEff# cd ~/wes_cancer/project/5.gatk/
(wes) root@1100150:~/wes_cancer/project/5.gatk# ll
total 10343627
drwxr-xr-x 4 root root 28 Jun 24 13:19 ./
drwxr-xr-x 14 root root 23 Jun 23 15:20 ../
-rw-r--r-- 1 root root 3668 Jun 23 03:55 9Y1640.metrics
-rw-r--r-- 1 root root 27369262 Jun 24 09:19 9Y1640WES.HC.vcf
-rw-r--r-- 1 root root 840988 Jun 24 09:19 9Y1640WES.HC.vcf.idx
-rw-r--r-- 1 root root 33954834 Jun 24 13:19 9Y1640WES.indel.VQSR.vcf
-rw-r--r-- 1 root root 799396 Jun 24 13:19 9Y1640WES.indel.VQSR.vcf.idx
-rw-r--r-- 1 root root 565 Jun 24 12:57 9Y1640WES.snp.indel.tranches
-rw-r--r-- 1 root root 2874463 Jun 24 12:50 9Y1640WES.snp.plots.R
-rw-r--r-- 1 root root 10608245 Jun 24 12:50 9Y1640WES.snp.recal
-rw-r--r-- 1 root root 350519 Jun 24 12:50 9Y1640WES.snp.recal.idx
-rw-r--r-- 1 root root 649 Jun 24 12:49 9Y1640WES.snp.tranches
-rw-r--r-- 1 root root 2900245 Jun 24 12:57 9Y1640WES_L1.snp.indel.plots.R
-rw-r--r-- 1 root root 5917328 Jun 23 06:47 9Y1640_bqsr.bai
-rw-r--r-- 1 root root 6737017862 Jun 23 06:47 9Y1640_bqsr.bam
-rw-r--r-- 1 root root 34486 Jun 23 06:47 9Y1640_log.ApplyBQSR
-rw-r--r-- 1 root root 95578 Jun 23 15:20 9Y1640_log.HC
-rw-r--r-- 1 root root 23673 Jun 23 03:55 9Y1640_log.mark
-rw-r--r-- 1 root root 55198 Jun 23 06:00 9Y1640_log.recal
-rw-r--r-- 1 root root 4918808 Jun 23 03:56 9Y1640_marked.bai
-rw-r--r-- 1 root root 3804215038 Jun 23 03:55 9Y1640_marked.bam
-rw-r--r-- 1 root root 57651909 Jun 23 15:20 9Y1640_raw.vcf
-rw-r--r-- 1 root root 12112891 Jun 23 15:20 9Y1640_raw.vcf.idx
-rw-r--r-- 1 root root 111005 Jun 23 06:00 9Y1640_recal.table
drwxr-xr-x 2 root root 6 Jun 24 12:57 data/
drwxr-xr-x 2 root root 4 Jun 24 00:18 gvcf/
-rw------- 1 root root 217 Jun 24 01:28 nohup.out
-rw-r--r-- 1 root root 0 Jun 23 03:55 ok.9Y1640_marked.status
(wes) root@1100150:~/wes_cancer/project/5.gatk# java -jar ~/wes_cancer/biosoft/snpEff/snpEff.jar GRCh38.86 9Y1640WES.indel.VQSR.vcf > test.9Y1640WES.ann.vcf
The annotation process was quite fast, taking less than 10 minutes. Let’s check the data before and after annotation:
(wes) root@1100150:~/wes_cancer/project/5.gatk# ll
total 10383925
drwxr-xr-x 4 root root 31 Jun 27 01:22 ./
drwxr-xr-x 14 root root 23 Jun 23 15:20 ../
-rw-r--r-- 1 root root 3668 Jun 23 03:55 9Y1640.metrics
-rw-r--r-- 1 root root 27369262 Jun 24 09:19 9Y1640WES.HC.vcf
-rw-r--r-- 1 root root 840988 Jun 24 09:19 9Y1640WES.HC.vcf.idx
-rw-r--r-- 1 root root 33954834 Jun 24 13:19 9Y1640WES.indel.VQSR.vcf
-rw-r--r-- 1 root root 799396 Jun 24 13:19 9Y1640WES.indel.VQSR.vcf.idx
-rw-r--r-- 1 root root 565 Jun 24 12:57 9Y1640WES.snp.indel.tranches
-rw-r--r-- 1 root root 2874463 Jun 24 12:50 9Y1640WES.snp.plots.R
-rw-r--r-- 1 root root 10608245 Jun 24 12:50 9Y1640WES.snp.recal
-rw-r--r-- 1 root root 350519 Jun 24 12:50 9Y1640WES.snp.recal.idx
-rw-r--r-- 1 root root 649 Jun 24 12:49 9Y1640WES.snp.tranches
-rw-r--r-- 1 root root 2900245 Jun 24 12:57 9Y1640WES_L1.snp.indel.plots.R
-rw-r--r-- 1 root root 5917328 Jun 23 06:47 9Y1640_bqsr.bai
-rw-r--r-- 1 root root 6737017862 Jun 23 06:47 9Y1640_bqsr.bam
-rw-r--r-- 1 root root 34486 Jun 23 06:47 9Y1640_log.ApplyBQSR
-rw-r--r-- 1 root root 95578 Jun 23 15:20 9Y1640_log.HC
-rw-r--r-- 1 root root 23673 Jun 23 03:55 9Y1640_log.mark
-rw-r--r-- 1 root root 55198 Jun 23 06:00 9Y1640_log.recal
-rw-r--r-- 1 root root 4918808 Jun 23 03:56 9Y1640_marked.bai
-rw-r--r-- 1 root root 3804215038 Jun 23 03:55 9Y1640_marked.bam
-rw-r--r-- 1 root root 57651909 Jun 23 15:20 9Y1640_raw.vcf
-rw-r--r-- 1 root root 12112891 Jun 23 15:20 9Y1640_raw.vcf.idx
-rw-r--r-- 1 root root 111005 Jun 23 06:00 9Y1640_recal.table
drwxr-xr-x 2 root root 6 Jun 24 12:57 data/
drwxr-xr-x 2 root root 4 Jun 24 00:18 gvcf/
-rw------- 1 root root 217 Jun 24 01:28 nohup.out
-rw-r--r-- 1 root root 0 Jun 23 03:55 ok.9Y1640_marked.status
-rw-r--r-- 1 root root 16479733 Jun 27 01:22 snpEff_genes.txt
-rw-r--r-- 1 root root 543550 Jun 27 01:22 snpEff_summary.html
-rw-r--r-- 1 root root 155714613 Jun 27 01:22 test.9Y1640WES.ann.vcf
(wes) root@1100150:~/wes_cancer/project/5.gatk# less -S 9Y1640WES.indel.VQSR.vcf |grep -v "#"|less -S |head
chr1 14574 . A G 159.64 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.653;DP=37;ExcessHet=3.0103;FS=2.663;MLEAC=1;MLEAF=0.500;MQ=30.00;MQRankSum=-4.861;QD=4.56;ReadPosRankSum=-0.128;SOR=1.539;VQSLOD=-2.769e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:25,10:35:99:167,0,647
chr1 14590 . G A 298.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=4.998;DP=48;ExcessHet=3.0103;FS=7.638;MLEAC=1;MLEAF=0.500;MQ=32.48;MQRankSum=-5.175;QD=6.22;ReadPosRankSum=1.525;SOR=2.670;VQSLOD=-6.174e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:38,10:48:99:306,0,1566
chr1 14599 . T A 291.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=50;ExcessHet=3.0103;FS=10.372;MLEAC=1;MLEAF=0.500;MQ=32.67;MQRankSum=-5.213;QD=5.83;ReadPosRankSum=1.614;SOR=3.014;VQSLOD=-7.996e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:40,10:50:99:299,0,1649
chr1 14604 . A G 399.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=3.537;DP=59;ExcessHet=3.0103;FS=12.817;MLEAC=1;MLEAF=0.500;MQ=33.70;MQRankSum=-4.818;QD=6.77;ReadPosRankSum=0.247;SOR=3.533;VQSLOD=-1.000e+01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:46,13:59:99:407,0,1872
chr1 14610 . T C 411.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=5.871;DP=66;ExcessHet=3.0103;FS=21.573;MLEAC=1;MLEAF=0.500;MQ=33.76;MQRankSum=-4.854;QD=6.33;ReadPosRankSum=0.367;SOR=4.266;VQSLOD=-1.804e+01;culprit=FS GT:AD:DP:GQ:PL 0/1:51,14:65:99:419,0,1958
chr1 14653 . C T 1074.64 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.334;DP=149;ExcessHet=3.0103;FS=6.839;MLEAC=1;MLEAF=0.500;MQ=37.03;MQRankSum=-2.288;NEGATIVE_TRAIN_SITE;QD=7.57;ReadPosRankSum=-3.040;SOR=1.266;VQSLOD=-2.512e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:89,53:142:99:1082,0,1965
chr1 14932 . G T 67.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.524;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.83;MQRankSum=-1.645;NEGATIVE_TRAIN_SITE;QD=13.53;ReadPosRankSum=1.036;SOR=1.609;VQSLOD=-4.508e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:3,2:5:75:75,0,120
chr1 14937 . T C 67.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.645;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.53;MQRankSum=-1.645;NEGATIVE_TRAIN_SITE;QD=13.53;ReadPosRankSum=1.036;SOR=1.609;VQSLOD=-3.674e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:3,2:5:75:75,0,120
chr1 15903 . G GC 585 PASS AC=2;AF=1.00;AN=2;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.15;QD=32.50;SOR=0.693;VQSLOD=3.54;culprit=FS GT:AD:DP:GQ 1/1:0,18:18:54:599,54,0
chr1 16378 . T C 51.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.204;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.26;MQRankSum=-2.189;NEGATIVE_TRAIN_SITE;QD=7.38;ReadPosRankSum=-1.718;SOR=0.495;VQSLOD=-4.642e+00;culprit=MQRankSum GT:AD:DP:GQ 0/1:4,3:7:59:59,0,98
(wes) root@1100150:~/wes_cancer/project/5.gatk# less -S test.9Y1640WES.ann.vcf |grep -v "#"|less -S |head
chr1 14574 . A G 159.64 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.653;DP=37;ExcessHet=3.0103;FS=2.663;MLEAC=1;MLEAF=0.500;MQ=30.00;MQRankSum=-4.861;QD=4.56;ReadPosRankSum=-0.128;SOR=1.539;VQSLOD=-2.769e+00;culprit=MQRankSum;ANN=G|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*165A>G|||||165|,G|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*2795T>C|||||2795|,G|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*904A>G|||||904|,G|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|10/10|n.1254-73T>C|||||| GT:AD:DP:GQ:PL 0/1:25,10:35:99:167,0,647
chr1 14590 . G A 298.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=4.998;DP=48;ExcessHet=3.0103;FS=7.638;MLEAC=1;MLEAF=0.500;MQ=32.48;MQRankSum=-5.175;QD=6.22;ReadPosRankSum=1.525;SOR=2.670;VQSLOD=-6.174e+00;culprit=MQRankSum;ANN=A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*181G>A|||||181|,A|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*2779C>T|||||2779|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*920G>A|||||920|,A|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|10/10|n.1254-89C>T|||||| GT:AD:DP:GQ:PL 0/1:38,10:48:99:306,0,1566
chr1 14599 . T A 291.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=50;ExcessHet=3.0103;FS=10.372;MLEAC=1;MLEAF=0.500;MQ=32.67;MQRankSum=-5.213;QD=5.83;ReadPosRankSum=1.614;SOR=3.014;VQSLOD=-7.996e+00;culprit=MQRankSum;ANN=A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*190T>A|||||190|,A|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*2770A>T|||||2770|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*929T>A|||||929|,A|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|10/10|n.1254-98A>T|||||| GT:AD:DP:GQ:PL 0/1:40,10:50:99:299,0,1649
chr1 14604 . A G 399.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=3.537;DP=59;ExcessHet=3.0103;FS=12.817;MLEAC=1;MLEAF=0.500;MQ=33.70;MQRankSum=-4.818;QD=6.77;ReadPosRankSum=0.247;SOR=3.533;VQSLOD=-1.000e+01;culprit=MQRankSum;ANN=G|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*195A>G|||||195|,G|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*2765T>C|||||2765|,G|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*934A>G|||||934|,G|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|10/10|n.1254-103T>C|||||| GT:AD:DP:GQ:PL 0/1:46,13:59:99:407,0,1872
chr1 14610 . T C 411.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=5.871;DP=66;ExcessHet=3.0103;FS=21.573;MLEAC=1;MLEAF=0.500;MQ=33.76;MQRankSum=-4.854;QD=6.33;ReadPosRankSum=0.367;SOR=4.266;VQSLOD=-1.804e+01;culprit=FS;ANN=C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*201T>C|||||201|,C|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*2759A>G|||||2759|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*940T>C|||||940|,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|10/10|n.1254-109A>G|||||| GT:AD:DP:GQ 0/1:51,14:65:99:419,0,1958
chr1 14653 . C T 1074.64 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.334;DP=149;ExcessHet=3.0103;FS=6.839;MLEAC=1;MLEAF=0.500;MQ=37.03;MQRankSum=-2.288;NEGATIVE_TRAIN_SITE;QD=7.57;ReadPosRankSum=-3.040;SOR=1.266;VQSLOD=-2.512e+00;culprit=MQRankSum;ANN=T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*244C>T|||||244|,T|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*2716G>A|||||2716|,T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*983C>T|||||983|,T|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|10/10|n.1254-152G>A|||||| GT:AD:DP:GQ 0/1:89,53:142:99:1082,0,1965
chr1 14932 . G T 67.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.524;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.83;MQRankSum=-1.645;NEGATIVE_TRAIN_SITE;QD=13.53;ReadPosRankSum=1.036;SOR=1.609;VQSLOD=-4.508e+00;culprit=MQRankSum;ANN=T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*523G>T|||||523|,T|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*2437C>A|||||2437|,T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*1262G>T|||||1262|,T|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|10/10|n.1253+73C>A|||||| GT:AD:DP:GQ 0/1:3,2:5:75:75,0,120
chr1 14937 . T C 67.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.645;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.53;MQRankSum=-1.645;NEGATIVE_TRAIN_SITE;QD=13.53;ReadPosRankSum=1.036;SOR=1.609;VQSLOD=-3.674e+00;culprit=MQRankSum;ANN=C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*528T>C|||||528|,C|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*2432A>G|||||2432|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*1267T>C|||||1267|,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|10/10|n.1253+68A>G|||||| GT:AD:DP:GQ 0/1:3,2:5:75:75,0,120
chr1 15903 . G GC 585.0 PASS AC=2;AF=1.00;AN=2;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.15;QD=32.50;SOR=0.693;VQSLOD=3.54;culprit=FS;ANN=GC|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*1494_*1495insC|||||1495|,GC|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*1465dupG|||||1465|,GC|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*2233_*2234insC|||||2234|,GC|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|9/11|n.1111dupG|||||| GT:AD:DP:GQ 1/1:0,18:18:54:599,54,0
chr1 16378 . T C 51.64 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.204;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.26;MQRankSum=-2.189;NEGATIVE_TRAIN_SITE;QD=7.38;ReadPosRankSum=-1.718;SOR=0.495;VQSLOD=-4.642e+00;culprit=MQRankSum;ANN=C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*1969T>C|||||1969|,C|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.*991A>G|||||991|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*2708T>C|||||2708|,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|8/10|n.1067+229A>G|||||| GT:AD:DP:GQ 0/1:4,3:7:59:59,0,98
Further analysis and interpretation of the annotated data require consulting the official documentation.