Re: [Samtools-help] Comparing .vcf files and calling SNPs

[Barris, W. <Wes...@co...>]

Mauricio Carneiro wrote on 2011-06-27:

> Hi Wes,
> 
> GATK has a tool that does exactly that. Here is an example:
> 
> Select all calls missed by dataset myCalls.vcf, but present on HapMap.
> Useful to take a look at why these variants weren't called by this
> dataset.

Thanks Mauricio.  Is there any more documentation on this function like maybe
a tutorial?  The SelectVariants web page assumes a certain level of knowledge
about the GATK that I do not have.  For example, how do I specify the values
in the -B option?  Is the name in the -disc option supposed to match the name
in the -B option?  What name should be supplied with the -sn option?  The
documentation just says "sample name", what is that?

I've tried running this but the output file just contains the same variants
as the input hapmap file so I must not be running it correctly.

> java -jar GenomeAnalysisTK.jar \
> 	-T SelectVariants \
> 	-R human_g1k_v37.fasta \
> 	-B:variant,VCF hapmap.vcf \
> 	-B:mycalls,VCF myCalls.vcf \
> 	-disc mycalls \
> 	-sn mySample \
> 	-o myMissedHapMapCalls.vcf
> 
> 
> More information in the gatk wiki:
> http://www.broadinstitute.org/gsa/wiki/index.php/SelectVariants
> 
> cheers,
> 
> Mauricio Carneiro, Ph.D. http://www.broadinstitute.org/~carneiro/
> 
> 
> 
> On Mon, Jun 27, 2011 at 9:33 AM, Barris, Wes <Wes.Barris@cobb-
> vantress.com> wrote:
>> I would like to generate two SNP lists and then find the difference
>> between these two lists.  This sounds easy enough but I think the
>> problem is more difficult than it first seems.
>> 
>> I have two sets of 30x Illumina paired end reads.  I have
>> independently aligned both sets to the genome and independently run
>> both sets through a samtools pipeline ending up with two .vcf files.
>> 
>> Many of the SNPs listed in these two .vcf files are the same but I'm
>> interested in the differences.
>> 
>> When I use tview to examine a SNP that is found in one animal but not
>> the other, the reason it is not called in the other animal is often
>> because of lower coverage (not enough reads covering the SNP in both
>> directions, etc.). However, I'm interested in SNPs that are in one
>> animal but definitely NOT in the other.  Can anyone suggest a way to
>> identify these SNPs? -- Wes Barris
>> 
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Wes Barris

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