VCF file ID missing
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20 months ago
tothepoint ▴ 620

I am working with WGS data and ran GATK pipeline. We are currently studying selective sweep gene study and I encountered this issue of missing id information. The ID position for each chromosome is . When we assumed it would be rs5254666 like information. Please share your experience what need to be done to fix this issue. I am stucked in the mid with no clue.

#CHROM  POS **ID**  REF ALT QUAL    FILTER  INFO    FORMAT  KB10    KB11    KB12    KB6  
1   112 **.**   C   T   349.40  PASS    AC=1;AF=0.050;AN=20;BaseQRankSum=2.48;DP=156;ExcessHet=3.0103;FS=0.000;InbreedingCoeff=-0.0529;MLEAC=1;MLEAF=0.050;MQ=45.54 ;MQRankSum=-1.010e-01;QD=18.39;ReadPosRankSum=0.899;SOR=0.836   GT:AD:DP:GQ:PL  0/0:17,0:17:48:0,48,720 0/0:12,0:12:33:0,33,495 0/0:16,0:16:48:0,48,698 0/0:10,0:10:24:0,24,360 0/0 :19,0:19:51:0,51,765    

1   134 **.**   G   T   349.44

1   203 **.**   C   T   349.4

I am looking for something:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 
20 14370 **rs6054257** G A 29 PASS

Thanks

SNP assembly VCF WGS • 651 views
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20 months ago
Yean ▴ 140

Check this: How to get SNP identifiers from VCF file?

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Thankyou for the quick response. I tried following this but ended up with no solution. Finally, I found bcftools annotate How to add rsID in vcf seems worked for me. I am now going to do post analysis hope this works for me. Thank you again for the help.

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