#46 Filtering a VCF with a BED file

[Yannick Renaud]

Hello,

A well formet bed file is in format +0 and +1 for the start and the end.
It seems that VCFtools considers a bed file to be in +1 and +0 format.
This is wrong and should be corrected...

Example
VCF have position (format +1)
chr 1 pos 10
chr 1 pos 21
BED have position (format +0, +1)
1 10 20
1 22 30

When using VCFtools to remove all variations not in the regions, VCFtools keep the 2 variations.

[Anthony Marcketta]

Hello Yannick,

I cannot replicate your error. Are you using the latest release of vcftools, version 0.1.11? Another possible issue could be that the sites in your vcf file are indels. If your sites span multiple bases, vcftools will include all possible positions of that site and check if they are within the BED file ranges. Could you produce sample files for me that this error occurs on?

[Yannick Renaud]

You seem to be right.
It is because of indels...
I am just used to tools like GATK or bedtools that only looks at the first
position.

Sorry for the inconvinience.

Yannick

On Fri, Dec 13, 2013 at 10:42 AM, Anthony Marcketta
amarcket@users.sf.netwrote:

Hello Yannick,

I cannot seem to replicate your error. Are you using the latest release of
vcftools, version 0.1.11? Another possible issue could be that the sites in
your vcf file are indels. If your sites span multiple bases, vcftools will
include all possible positions of that site and check if they are within
the BED file ranges. Could you produce sample files for me that this error
occurs on?

---

• [bugs:#46] http://sourceforge.net/p/vcftools/bugs/46/ Filtering a VCF
  with a BED file*

Status: open
Labels: BED filtering
Created: Thu Dec 12, 2013 10:44 PM UTC by Yannick Renaud
Last Updated: Thu Dec 12, 2013 10:44 PM UTC
Owner: Adam Auton

Hello,

A well formet bed file is in format +0 and +1 for the start and the end.
It seems that VCFtools considers a bed file to be in +1 and +0 format.
This is wrong and should be corrected...

Example
VCF have position (format +1)
chr 1 pos 10
chr 1 pos 21
BED have position (format +0, +1)
1 10 20
1 22 30

When using VCFtools to remove all variations not in the regions, VCFtools
keep the 2 variations.

---

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