Comparing two BAM files for variant calling

Question

[Yogesh]

Hi,

I have two bam files corresponding to genomes of two related species A and B. Both bam files have been mapped to a common third reference genome C. Now I want to call variants between A and B. Can someone suggest a workflow? Are there tools to compare bam files directly for indels, SNPs etc?

[GenoMax]

i want to call variants between A and B

Not quite. You want to see what variants are common/different between the two VCF files. For that you can use bcftools isec . See How bcftools isec works ?

[Yogesh]

thank you for response. i actually have two bam files for now which i want to compare to each other and predict SNPs.

[GenoMax]

You can't compare BAM files directly. You will need to call variants from the files and compare the VCF's.