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Old 12-12-2012, 02:58 PM   #26
rama
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Location: Boston, USA

Join Date: Jan 2011
Posts: 20
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Hi Laura,

I am still having trouble with extracting the variant calls of a specific sample.

As you pointed out earlier that I have downloaded sites file with no genotype column, so now I got this version ALL.2of4intersection.20100804.genotypes.vcf.gz vcf and tbi file from ftp site (release/20100804).

and I used the following command to subset the vcf file

tabix -fh /Volumes/Macintosh_HD_3/1000Genome/ALL.2of4intersection.20100804.genotypes.vcf.gz 1 | perl ~/othertools/vcftools_0.1.10/perl/vcf-subset -c NA10851 > NA10851/NA10851_chr1

but strangely the out-put file has all genotype columns. I have been following the directions given on the 1000 genome except the I don't give the range for chromosome as I want to get all variants. So I tried with giving the coordinates (see below) and result file has just the header only.

here is the command i used,
tabix -fh /Volumes/Macintosh_HD_3/1000Genome/ALL.2of4intersection.20100804.genotypes.vcf.gz 2:1-243199373 | perl ~/othertools/vcftools_0.1.10/perl/vcf-subset -c NA10851 > NA10851/NA10851_chr2

so now I really don't know what I am doing wrong in trying to subset the vcf file. I really appreciate for your kind help so far and would be very grateful if you could help me how to solve this.

thank you so much.
Rama
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