Question

Convert Bed To Vcf4.0

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13.2 years ago

Bair • 0

Hi here,

I have genotype in bed format, how can I convert it into vcf4.0 format? thanks

bed vcf conversion • 7.5k views

ADD COMMENT • link updated 13.2 years ago by Hypotheses ▴ 90 • written 13.2 years ago by Bair • 0

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try 'awk'

ADD REPLY • link 13.2 years ago by Pierre Lindenbaum 161k

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Do you mean PLINK's BED (binary PED) format or UCSC BED format?

ADD REPLY • link 12.1 years ago by Aaronquinlan 12k

score 1 · Answer 1 · 2011-02-04

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13.2 years ago

Swatchpuppy ▴ 50

Daniel,

Have you checked this:

http://vcftools.sourceforge.net/options.html

Hope it helps,
SwatchPuppy

ADD COMMENT • link 13.2 years ago by Swatchpuppy ▴ 50

score 0 · Answer 2 · 2012-04-01

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12.1 years ago

Hypotheses ▴ 90

Daniel, have you found the answer? The only way I found right now is to use plink/seq, but there is some problem with setting the reference-allele that I haven't found the answer yet.

ADD COMMENT • link 12.1 years ago by Hypotheses ▴ 90