remove vcf variants from bam

Question

[Anst]

Hello!

Is there any way of changing all variants, which are listed in vcf file, in bam file? If there are several alleles, we take random one from them and place one the position in bam file.

Thanks!

[Pierre Lindenbaum]

just curious : why would you want to do this ?

[Anst]

to get rid of calling "mistakes"

[JC]

can remove by QUAL or other filtering options?

[brunobsouzaa]

You can use --annotations-to-exclude from HaplotypeCaller and exclude those regions for Variant Call.