how to use vcf2bed with .gz file

Question

[Medhat]

Is there is a way to use vcf2bed with compressed file?

for example in general the tool work like this

vcf2bed < foo.vcf > sorted-foo.vcf.bed

so if my file is foo.vcf.gz

zcat foo.vcf.gz | vcf2bed > sorted-foo.vcf.bed

will not work any idea?

Answer 1

[Pierre Lindenbaum]

( not tested ) using a hyphen for stdin ?

zcat foo.vcf.gz | vcf2bed - > sorted-foo.vcf.bed

or

vcf2bed <(gunzip -c foo.vcf.gz) > sorted-foo.vcf.bed

?

[Medhat]

That is right the first form zcat foo.vcf.gz | vcf2bed - > sorted-foo.vcf.bed worked fine; the other did not,

Please change to an answer :)