I have two vcf files that file names are A.vcf and B.vcf.
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleB SampleA chr1 762560 SNV_1 G T . . . GT:AD:DP:RGQ 0/0:31,0:31:81:0,81,1215 0/1:18,12:30:99:375,0,544
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleB SampleA chr1 762560 SNV_2 G . . . . GT:DP:RGQ 0/0:19:51 0/0:23:63
As you see above, SNV_1 in A.vcf and SNV_2 in B.vcf are SNVs on the same position. However SNV_1 has Alt info "T", but SNV_2 doesn't have Alt info. Thus, SNV_2 in B.vcf doesn't have AD info in genotype data.
I would like to know how to merge these two vcf files into one vcf file, recognizing SNV_A and SNV_B as same variant data.
Could you give me any advice?