Question

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

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2.5 years ago

taniamahmood38 ▴ 60

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

ancestral_allele vcf bam • 871 views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 2.5 years ago by taniamahmood38 ▴ 60

score 1 · Answer 1 · 2022-05-24

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2.5 years ago

Ram 44k

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

ADD COMMENT • link 2.5 years ago by Ram 44k

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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.

ADD REPLY • link 2.5 years ago by taniamahmood38 ▴ 60

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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.