Is there a way to call variants from a BAM file based of a list of position ?

[dickie_ho]

Hey all

Just trying to find a way to call around 100,000 single-point positions from BAM files calling both mismatches from the reference genome and also homozygous to the reference.

I can't call every variant in WGS data(and then filter) as the file size for every individual will be huge

Ideas ??

Cheers

Josh

[bruce01]

You could take just those positions from the BAM using samtools view, and call variants on this BAM, or if you use GATK you can specify --intervals/-L in BED format for the required positons. Depends on how you are calling the variants, I imagine callers will have a 'regions' input.

[dickie_ho]

Thanks Bruce

Will give that a shot, somehow I overlooked the intervals argument