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Old 06-04-2013, 04:01 AM   #1
Location: barcelona

Join Date: Mar 2013
Posts: 18
Question vcf files merging

Hi all,

I was wondering which is the easiest way to merge multiple vcf files (outputs of Varscan). I have some vcf files listing all the called snps for an individual (1 snp per line). I would like to put together all this info in a n output that shows for every line a snp (original base, variant base/bases, and eventually number of individuals sharing the variant).
I tried with GATK CombineVariants and had the ouput I wanted, but in case of different variant at the same position, only one of the variant bases was reported.

I am working on a Mac's Terminal, OS 10.6.

If needed I have access also to a Linux OS.

Thanks in advance!
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Old 06-04-2013, 04:08 AM   #2
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Old 06-04-2013, 07:33 AM   #3
Location: barcelona

Join Date: Mar 2013
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Sorry GenoMax, I forgot to mention that I tried vcftools/vcf-merge, but still the output does not show different variants for the same position.
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Old 06-13-2013, 06:30 AM   #4
Location: Saint Louis

Join Date: Jul 2011
Posts: 26

You could try joinx's vcf-merge command which I'm fairly confident reports multiple variant alleles at a position.

The code is available as a debian package from: but you may want to compile from source code (the github page is linked off the gmt page).
ernfrid is offline   Reply With Quote

osx, varscan, vcf, vcftools

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