Question: how to use vcf2bed with .gz file
0
gravatar for Medhat
2.3 years ago by
Medhat8.4k
Texas
Medhat8.4k wrote:

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?

snp next-gen vcf • 718 views
ADD COMMENTlink written 2.3 years ago by Medhat8.4k
1
gravatar for Pierre Lindenbaum
2.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k wrote:

( 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

?

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Pierre Lindenbaum122k
1

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 :)

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Medhat8.4k
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