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Getting The Vcf Consensus For Only A Segment Of The Genome

I have numerous VCF files of a HIV genomic region and I'm looking to retrieve the resulting consensus sequence from just a region ~50 nt of the alignment so I can feed it to a TF binding prediction program. Normally I'd just use vcf-consensus to output the whole region and then slice the region I want out. However, there are numerous indels (of varying sizes) in this region that are important and I don't want to use that sort of method.

I can't seem to find any flags in the vcf-consensus tool that lets me limit the output.

Any suggestions?

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updated by swbarnes2 swbarnes2 • written by Will Will

1 answer

Aside from awk? You can use BEDTools to get the intersect of a vcf and a .bed file with your region.

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written by swbarnes2 swbarnes2

I can easily filter the VCF to get my desired region. But if there are insertions wouldn't bedtools-intersect just give me the 50nt region and not 50 nt + insertions?

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updated by Ram Ram • written by Will Will

Will, how did you solved this? How did you filter the desired region in a .vcf? Thanks!

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written by boludopublico • boludopublico

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