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Old 11-29-2011, 08:15 AM   #1
gavin.oliver
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Default 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.
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Old 11-29-2011, 01:39 PM   #2
aslihan
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you can use samtools mpileup to compare 2 vcf files at the same time.
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Old 11-29-2011, 02:21 PM   #3
swbarnes2
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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.
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Old 11-30-2011, 03:16 AM   #4
gavin.oliver
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BEDTools appears to be what I am after - cheers!
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