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