Question: Vcf annotate does not work
1
gravatar for fireprophet.io
8 months ago by
fireprophet.io10 wrote:

Hello, colleagues!

Could you, please, help or give a hint what's wrong?

My HaplotypeCaller and VariantFiltration tools are Version=3.4-46-gbc02625

Java used is: jre1.8.0_231

I use the following command:

cat our.vcf | vcf-annotate -a home/dbSNP/All_20180418.vcf.gz -d key=INFO,ID=ANN,Number=1,Type=Integer,Description='dbSNP' -c CHROM,POS,ID,REF,ALT,-,-,- > our.dbSNP.vcf

I have no log after calling the command (maybe I do not know where the log is written). Command line returns in few seconds (obviously nothing is done through these moments) with exact vcf file which i gave to the command as input.

I use All_20180418.vcf.gz with index file All_20180418.vcf.gz.tbi from National Library of Medicine (ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/ ) in the same folder.

The titles of my input vcf file and the brief content is below:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT OncoUnite
chr1 113249 . AC A 38.70 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=19.35;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0
snp • 403 views
ADD COMMENTlink modified 8 months ago by RamRS30k • written 8 months ago by fireprophet.io10
1
gravatar for Pierre Lindenbaum
8 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

NCBI uses the chromosome without "chr" prefix:

$ wget  -q -O - "ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/All_20180418.vcf.gz" | gunzip -c | grep -v "^##" | cut -f1 | head
#CHROM
1
1
1
1
1
1
1
1
1

while your vcf starts with chr

chr1 113249 . AC A 38.70 PASS

Change the chr notation:

ADD COMMENTlink modified 8 months ago by zx87549.6k • written 8 months ago by Pierre Lindenbaum130k

Dear Pierre! Thank you! It helps! For the most rows a get annotations, at the same time I did not get annotations for mitochondrial chromosome chrM (after deletion of chr prefix it is M)... What is the reason for this issue?

M 11719 . G A 100.28 PASS AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.43;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,3:3:9:128,9,0 M 11866 . AC A 14.87 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.97;ReadPosRankSum=1.026;SOR=0.693 GT:AD:DP:GQ:PL 0/1:2,2:4:52:52,0,52 M 11978 . TC T 21.76 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=1.026;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=4.35;ReadPosRankSum=1.026;SOR=2.303 GT:AD:DP:GQ:PL 0/1:2,2:4:59:59,0,59 M 12501 . G A 101.28 PASS AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.76;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,3:3:9:129,9,0 M 12605 . TC T 21.76 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=4.35;ReadPosRankSum=0.000;SOR=0.693 GT:AD:DP:GQ:PL 0/1:2,2:4:59:59,0,59 M 12668 . AC A 79.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.638;ClippingRankSum=0.922;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.421;QD=9.97;ReadPosRankSum=1.368;SOR=0.148 GT:AD:DP:GQ:PL 0/1:4,4:8:99:117,0,118 M 12701 . TC T 13.91 LowQual;QD;SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=0.898;ClippingRankSum=0.480;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=1.39;ReadPosRankSum=-0.480;SOR=0.105 GT:AD:DP:GQ:PL 0/1:8,2:10:51:51,0,312 M 12705 . C T 335.22 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-1.739;ClippingRankSum=-1.107;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.423;QD=30.47;ReadPosRankSum=-1.107;SOR=3.442 GT:AD:DP:GQ:PL 0/1:1,10:11:4:362,0,4 M 12720 . AC A 25.74 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-1.179;ClippingRankSum=0.762;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.179;QD=2.86;ReadPosRankSum=0.067;SOR=0.132 GT:AD:DP:GQ:PL 0/1:7,2:9:63:63,0,278 M 12726 . CT C 28.74 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-0.922;ClippingRankSum=0.922;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.198;QD=4.11;ReadPosRankSum=-0.198;SOR=0.223 GT:AD:DP:GQ:PL 0/1:5,2:7:66:66,0,241 M 12733 . AC A 14.87 LowQual;QD;SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-0.922;ClippingRankSum=-1.495;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.198;QD=1.86;ReadPosRankSum=-0.922;SOR=0.223 GT:AD:DP:GQ:PL 0/1:5,2:7:52:52,0,189 M 12940 . GC G 34.71 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=17.35;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 M 13780 . A G 103.28 PASS AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.43;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,3:3:9:131,9,0 M 13847 . TC T 19.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.572;ClippingRankSum=-1.067;DP=8;FS=9.700;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.47;ReadPosRankSum=0.572;SOR=2.209 GT:AD:DP:GQ:PL 0/1:6,2:8:57:57,0,218 M 13980 . GC G 85.79 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.731;ClippingRankSum=0.731;DP=6;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.731;QD=14.30;ReadPosRankSum=-0.731;SOR=1.447 GT:AD:DP:GQ:PL 0/1:1,4:5:19:123,0,19 M 14056 . TC T 22.75 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=-0.358;DP=6;FS=10.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.358;QD=3.79;ReadPosRankSum=1.231;SOR=2.204 GT:AD:DP:GQ:PL 0/1:3,2:5:60:60,0,97 M 14114 . TCC T 53.70 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=26.85;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 M 14189 . AC A 23.75 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.720;ClippingRankSum=-0.720;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=3.96;ReadPosRankSum=0.720;SOR=0.693 GT:AD:DP:GQ:PL 0/1:4,2:6:61:61,0,141 M 14480 . AC A 22.75 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;ClippingRankSum=1.231;DP=5;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.358;QD=4.55;ReadPosRankSum=-1.231;SOR=0.061 GT:AD:DP:GQ:PL 0/1:3,2:5:60:60,0,97 M 14488 . TC T 45.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=-1.231;DP=7;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.231;QD=6.53;ReadPosRankSum=-0.727;SOR=2.833 GT:AD:DP:GQ:PL 0/1:2,3:5:51:83,0,51 M 14914 . AC A 28.74 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DP=4;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-0.736;QD=7.19;ReadPosRankSum=0.736;SOR=2.225 GT:AD:DP:GQ:PL 0/1:1,2:3:28:66,0,28 M 15043 . G A 98.28 PASS AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.76;SOR=2.833 GT:AD:DP:GQ:PL 1/1:0,3:3:9:126,9,0 M 15326 . A G 230.84 PASS AC=2;AF=1.00;AN=2;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.26;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,6:6:18:259,18,

ADD REPLYlink written 8 months ago by fireprophet.io10

check the names chrM, chMT, MT ...

ADD REPLYlink written 8 months ago by Pierre Lindenbaum130k

Sir, it helps! the notation in dbSNP is MT.

ADD REPLYlink written 8 months ago by fireprophet.io10
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