Intersecting compressed gVCF with bed file

Question

[graeme.thorn]

This may be a ridiculously simple question to ask but, I have a compressed genomic VCF file generated by the Strelka germline variant caller, with lines like the following, where no variation was detected:

chr1    27394730    .   T   .   .   PASS    END=27394756;BLOCKAVG_min30p3a  GT:GQX:DP:DPF:MIN_DP    0/0:3070:1137:14:1122

I need to intersect this with a set of regions I'm interested in. I have tried using bedtools intersect with a suitable BED file, but this only matches the the start of this blocked region at chr1 27394730 and not the remainder of the interval chr1:27394730-27394756.

Is there a way to run this intersection using bedtools?

I would think there's a way to do this by converting the gVCF into a BED file (preserving the variations that Strelka has found), but if there's a tool that can do this directly, then please point me in that direction

Answer 1

[Pierre Lindenbaum]

bcftools view --regions-file in.bed in.vcf.gz

[graeme.thorn]

Thanks. Is there a way of stating which region overlaps with the vcf using bcftools view?

I'm sort of looking for the kind of output you get with bedtools using the -wa and -wb flags.

[Pierre Lindenbaum]

not, that's a job for bcftools annotate with an annotation as an indexed bed.gz.