Question

bedtools on vcf.gz file

2

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8.5 years ago

qmemcm ▴ 30

Can bedtools work directly on vcf.gz file, or do you have to first convert this into a vcf file?

bedtools vcf • 7.3k views

ADD COMMENT • link updated 8.5 years ago by Ram 44k • written 8.5 years ago by qmemcm ▴ 30

1

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Why don't you just check ?

ADD REPLY • link 8.5 years ago by GouthamAtla 12k

score 5 · Accepted Answer · 2016-06-20

5

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8.5 years ago

igor 13k

Yes.

bedtools will process gzipped BED, GFF, VCF and BEDPE files in the same manner as uncompressed files. Gzipped files are auto-detected thanks to a helpful contribution from Gordon Assaf.

http://bedtools.readthedocs.io/en/latest/content/overview.html

ADD COMMENT • link 8.5 years ago by igor 13k