Filter Alt Reads from BAM at List of Known Het Sites

Question

[alongalor]

I would like to remove all reads in a BAM that contain an alternate allele at a list of known heterozygous sites. Would appreciate any advice on how to best do this/which tools/commands to use. Thanks a lot!

Answer 1

[h.mon]

VariantBam.

BAMQL.

Extracting Reads Containing A Specific Variant From A Bam File

[alongalor]

Thanks for your response, h.mon. Seems straightforward to extract reads in a BAM that contain an alternate allele at a list of known heterozygous sites using these tools and the post you linked to but I'm not sure how I'd go about filtering them out. Any guidance would be much appreciated. Thanks

[finswimmer]

Hello alongalor,

before go on working on this, could you please tell us why you would like to this?

fin swimmer

[alongalor]

Sorry finswimmer, Unfortunately I'm not able to share this for privacy reasons. I do think the problem is very clear based on the way I have described it and could have a variety of good use-cases. Thanks!