Output a vcf restricted to variant sites listed in a file
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5.7 years ago

I'm looking for a tool that will output a vcf restricted to variant sites (not genomic intervals) listed in a tab-delimited file. I understand GATK SelectVariants can do this, but I'd prefer an alternative tool that doesn't reorder samples.

vcf SNP • 1.9k views
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3
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5.7 years ago

Not quite sure I understand why this won't work, as long as your bed file is composed of 1bp variant sites and not intervals.

bedtools intersect -a my.vcf -b my.bed -wa >output


If you have something different in mind, then example data would be helpful.

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this works nice, but is there a way to keep the vcf metadata so i can pipe to bcftools?

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Do you mean the header?  A couple of redirects will get you there:

cat <(head -n 10000 my.vcf | grep "^#") <(bedtools intersect -a my.vcf -b my.bed -wa) | downstreamToolX
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great, thanks!

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5.7 years ago

convert your vcf / target region to bed. (For a VCF it's something like:

grep -v "^#" your.vcf | awk -F '\t' '{printf("%s\t%d\t%d\n",$1,int($2)-1,int($2)+length($4)-1);}' > input.bed

and then use 'bcftools view' with option --regions-file

or

bedtools intersect..

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