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Old 04-19-2012, 05:48 AM   #1
info_nowise
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Location: New York

Join Date: Feb 2012
Posts: 4
Default vcftools site filter using bedfile

Hi all

I am trying to filter my vcf file in vcftools using a bed file. I am consistently getting an output vcf with 0 sites retained. Following is the command line I used:

vcftools --gzvcf myfile.vcf.gz --recode --bed bedfile.bed --out outfile

The log file looks like this:
VCFtools - v0.1.6
(C) Adam Auton 2009
Parameters as interpreted:
--out PsvaMvd7a
--recode
--gzvcf PsvaMvd7.vcf.gz
--bed CF2_probes_mod_sorted.bed

Scanning PsvaMvd7.vcf.gz ...
Currently scanning CHROM: MT
Currently scanning CHROM: 38
Currently scanning CHROM: 35
Currently scanning CHROM: 36
Currently scanning CHROM: 37
Currently scanning CHROM: 33
Currently scanning CHROM: 32
Currently scanning CHROM: 26.......
Keeping 1718454 entries (out of 1718454 read)
Done
Filtering sites by BED file
Kept 14 out of 14 Individuals
Kept 0 out of 1718454 Sites
Error:No data left for analysis!

My bed file looks like this:

"track name=""tiled_region"" description=""NimbleGen Tiled Regions"""
chr1 11398149 11398377
chr1 11398197 11398414
chr1 11398377 11398448
chr1 11453954 11454357
chr1 11453999 11454327
chr1 11456016 11456508
chr1 11456061 11456496
chr1 11537417 11537695
chr1 11537488 11537637

Appreciate any help. Thanks.

Last edited by info_nowise; 04-19-2012 at 05:58 AM. Reason: added more info
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Old 04-19-2012, 10:15 AM   #2
swbarnes2
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Location: San Diego

Join Date: May 2008
Posts: 912
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Are you 100% sure that's wrong?

BEDTools can also get you the intersect between a .vcf and a .bed
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Old 04-19-2012, 12:55 PM   #3
info_nowise
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Location: New York

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Yes, I am sure. However, I figured out the problem. I got rid of the letters 'chr' in the bed file, leaving only the numbers and vcftools worked!
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Old 04-19-2012, 12:56 PM   #4
info_nowise
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Thanks for the tip, though, swbarnes2!
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