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 ?
