Re: [Vcftools-help] Filtering by multiple chromosomes

[Anthony M. <ant...@ei...>]

Mike,

You should update to a newer version of vcftools. The ability to filter by multiple chromosomes was not introduced yet in v0.1.10.

Let me know if you need any further assistance.

--
Anthony Marcketta
Bioinformatics Analyst
Department of Genetics
Albert Einstein College of Medicine
Van Etten B01
Bronx, New York 10461
________________________________________
From: Michael Fletcher [mic...@tu...]
Sent: Wednesday, April 09, 2014 10:03 AM
To: vcf...@li...
Subject: [Vcftools-help] Filtering by multiple chromosomes

G'day,

I'm trying to filter a vcf with a list of chromosomes, like so:
===
$ vcftools --vcf SMIJ_5266.recal.unfiltered.vcf --recode-INFO-all --chr
chr1 --chr chr2 --chr chr3 --chr chr4 --chr chr5 --chr chr6 --chr chr7
--chr chr8 --chr chr9 --chr chr10 --chr chr11 --chr chr12 --chr chr13
--chr chr14 --chr chr15 --chr chr16 --chr chr17 --chr chr18 --chr chr19
--chr chrX --out SMIJ_5266.recal.contigfiltered.unfiltered
===

According to the man pages, this should pass every chromosome specified
by --chr ("These options may be used multiple times to include or
exclude more than one chromosome.").

However, when I run vcftools it only interprets the final --chr option
(--chr chrX):

===
VCFtools - v0.1.10
(C) Adam Auton 2009

Parameters as interpreted:
         --vcf SMIJ_5266.recal.unfiltered.vcf
         --chr chrX
         --recode-INFO-all
         --out SMIJ_5266.recal.contigfiltered.unfiltered.vcf
===

I'm probably missing something obvious here but is there a way to pass a
list of chromosomes? (I've tried using --positions with a single-column
text file of the chromosomes, but that doesn't appear to work either).

Thanks very much,

- Mike

--
-----
Mike Fletcher

Postdoctoral Fellow, Chan Group
Friedrich Miescher Laboratory of the Max Planck Society
Spemannstr. 39
72076 Tübingen
Germany

T: +49 (0)7071 601 887
@: mic...@tu...
http://www.fml.tuebingen.mpg.de/chan-group.html
-----

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