Merging vcf files

[kjaja]

I am noticing a problem when merging two VCF file if the SNP is multiallelic, below is an example of how a multiallelic SNP should look like in a VCF file for the merged samples. You can see that the AF= Allele frequency below takes two values (0.333, 0.667) which corresponds to the frequency of Alternative allele “G” and the “T” .

1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4

The problem that I am having is when merging two samples, I do not get AF values for each alternative allele. I tried to do this using VCF tools, below is my command.

perl vcf-merge file1.vcf.gz file2.vcf.gz >merged_files.vcf

Does anyone know how to solve this problem or if there are other tools to merge .vcf files that takes care of this problem?

Thanks,