Question: How to merge INFO fields in some files using GATK CombineVariants
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gravatar for Apprentice
3.1 years ago by
Apprentice30
Apprentice30 wrote:

Hi.

I would like to merge two vcf files (a.vcf, b.vcf) into one vcf file (c.vcf) using GATK CombineVariants.

a.vcf and b.vcf are shown as below;

$ cat a.vcf

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA

chr1 11077009 . C . . PASS VAR_ID=a_1 GT:DP:RGQ 0/0:33:99 chr2 74592269 . G . . PASS VAR_ID=a_2 GT:DP:RGQ 0/0:22:60

$ cat b.vcf

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleB

chr1 11077009 . C . . PASS VAR_ID=b_1 GT:DP:RGQ 0/0:35:99 chr2 74592269 . G A . PASS VAR_ID=b_2 GT:AD:DP:GQ:PL 0/0:42,0:42:99:0,111,1205

Finaly, I want to get c.vcf using GATK CombineVariants as below; $ cat c.vcf

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB

chr1 11077009 . C . . PASS VAR_ID=a_1,b_1 GT:DP:RGQ 0/0:33:99 0/0:35:99 chr2 74592269 . G A . PASS VAR_ID=a_2,b_2 GT:AD:DP:GQ:PL 0/0:22,0:60,0:: 0/0:42,0:42:99:0,111,1205

Please note that two vcf files have different VAR_ID values in INFO field, and I hope that both VAR_ID values are merged. How should I merge the files ?

snp sequence • 1.1k views
ADD COMMENTlink written 3.1 years ago by Apprentice30
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