pileup analysis

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pileup analysis

andrea_bio
Hello

I was wondering if there was anything available within galaxy that would
let you do the following with pileup files:

1) filter for homozygous SNVs (i.e. that do not contain the reference
genome allele in the genotype)
2) compare the pileup files for 2 (or more) individuals to find SNVs
unique to each individual and to further limit this to homozygous SNPs
unique to each individual
3) compare the pileup files for 2 (or more) individuals to find shared
SNVs and to further limit to this to shared SNVs where the individuals
have different alleles (rare as would assume triallelic snv) and then
group the individuals according to the allele for each SNV.

I could only see the filter pileup tool but nothing for comparing pileup
files

thanks
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Re: pileup analysis

Anton Nekrutenko
Dear Andrea:

Many apologies for a delay answering this. We are currently in the process of shifting genotyping pipelines to use VCF format, which, combined with a set of VCF manipulation utilities, will make it quite easy to perform operations you request. These should be ready for use by the end of Summer.

Thanks for using Galaxy,

anton
galaxy team


Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



On May 18, 2011, at 7:39 PM, Andrea Edwards wrote:

> Hello
>
> I was wondering if there was anything available within galaxy that would let you do the following with pileup files:
>
> 1) filter for homozygous SNVs (i.e. that do not contain the reference genome allele in the genotype)
> 2) compare the pileup files for 2 (or more) individuals to find SNVs unique to each individual and to further limit this to homozygous SNPs unique to each individual
> 3) compare the pileup files for 2 (or more) individuals to find shared SNVs and to further limit to this to shared SNVs where the individuals have different alleles (rare as would assume triallelic snv) and then group the individuals according to the allele for each SNV.
>
> I could only see the filter pileup tool but nothing for comparing pileup files
>
> thanks
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/