Comparing and combining vcf files

gavin.oliver · 11-29-2011, 08:15 AM

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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11-29-2011, 08:15 AM	#1
gavin.oliver Senior Member Location: uk Join Date: Jan 2010 Posts: 110	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.

11-29-2011, 01:39 PM	#2
aslihan Member Location: USA Join Date: Jun 2011 Posts: 23	you can use samtools mpileup to compare 2 vcf files at the same time.

11-29-2011, 02:21 PM	#3
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	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.

11-30-2011, 03:16 AM	#4
gavin.oliver Senior Member Location: uk Join Date: Jan 2010 Posts: 110	BEDTools appears to be what I am after - cheers!