Question: Getting The Vcf Consensus For Only A Segment Of The Genome
gravatar for Will
6.5 years ago by
United States
Will4.5k wrote:

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?

ADD COMMENTlink modified 6.5 years ago by swbarnes28.6k • written 6.5 years ago by Will4.5k
gravatar for swbarnes2
6.5 years ago by
United States
swbarnes28.6k wrote:

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

ADD COMMENTlink written 6.5 years ago by swbarnes28.6k

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?

ADD REPLYlink modified 9 months ago by RamRS30k • written 6.5 years ago by Will4.5k

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

ADD REPLYlink written 2.4 years ago by boludopublico0
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