How to generate bam to vcf containing ancestral allele (AA) information?

Question

[taniamahmood38]

Dear all, I am trying to find a way to make a vcf file having ancestral allele information in it from bam file on linuxOS. Kindly let me know the command and tool which can carry out this task? Any help would be highly appreciated.

Thanks in advance

Answer 1

[Ram]

1. Call variants and get the VCF file
2. Find a data source with ancestral allele information
3. Annotate above VCF file with that information.

[taniamahmood38]

Thank you so much for your guidance. Can you please guide me from where can I get the goat's ancestral allele file? Really sorry to bother again but I am badly stuck at this point.

[Ram]

I'm not sure how well studied goat is. There was no mention of the organism in your original post so I thought you were referring to human DNA. The protocol still applies, but I'm not conversant with genomic resources for goat. I can see that Ensembl has ancestral allele info for humans, not sure if anyone has ancestral allele info for goat.

[taniamahmood38]

Alright, many thanks for your guidance.