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-   -   Comparing and combining vcf files (http://seqanswers.com/forums/showthread.php?t=15858)

gavin.oliver 11-29-2011 08:15 AM

Comparing and combining vcf files
 
Hi,

I am trying to determine if there is an available solution for comparing vcf files and combining them into a single, non-redundant file?

So for example, if I have two vcf files for two patients, I would like to create one unique list of all the mutated locations observed in their genomes. Is there anything else out there or should I just script something?

Thanks in advance.

aslihan 11-29-2011 01:39 PM

you can use samtools mpileup to compare 2 vcf files at the same time.

swbarnes2 11-29-2011 02:21 PM

So you want the union of both files? Try vcftools or BEDTools.

I don't think that mpileup will work with vcf files. What it will allow you to do is to take multiple .bams at once, and make one multi-vcf. But if you don't have the .bams, that won't help much.

gavin.oliver 11-30-2011 03:16 AM

BEDTools appears to be what I am after - cheers!


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