Question: Getting The Vcf Consensus For Only A Segment Of The Genome
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gravatar for Will
5.6 years ago by
Will4.5k
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?

• 1.4k views
ADD COMMENTlink modified 5.6 years ago by swbarnes26.9k • written 5.6 years ago by Will4.5k
0
gravatar for swbarnes2
5.6 years ago by
swbarnes26.9k
United States
swbarnes26.9k 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 5.6 years ago by swbarnes26.9k

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 written 5.6 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 18 months ago by boludopublico0
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