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Question: Filtering for SNP genotype
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gravatar for d.angra
3.7 years ago by
d.angra • 50
United Kingdom
d.angra • 50 wrote:

I am a relatively new to galaxy. I have so far succeeded in using galaxy to discovery SNPs using SAM tools with my datasets with frequent help from galaxy team. Now that I have generated about 1 lakh SNPs I want to select only the ones from the set which have genotype specification 0/1 and hence heterozygotes only. Is there any tool which can help me select desired SNPs?

Your help will be greatly appreciated.
samtools • 1.2k views
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modified 3.5 years ago • written 3.7 years ago by d.angra • 50

Hello Mark,

Thankyou very much. I am trying this now.

 

Viva

ADD REPLY • link written 3.5 years ago by d.angra • 50
1
gravatar for Mark Crowe
3.6 years ago by
Mark Crowe • 100
QFAB, Brisbane
Mark Crowe • 100 wrote:

Hopefully someone else might come up with a more elegant solution, but a quick hack to do this might simply be to filter the VCF files for "0/1" at the beginning of column 10. In theory, you should be able to do this using the Filter tool with a filter condition of:

c10.split(":")[0]=="0/1"

This splits column 10 on the : character, and then only returns lines with 0/1 as the first string in that separation (first being index position zero, hence the [0])

But in testing, I've found some VCF files that this doesn't work for (possibly a bug in the filter or split function). If you get that, you could try the even cruder approach, using the Select tool to search for 

\t0/1

This just looks for the string 0/1 immediately after a tab character (i.e. at the beginning of a column field), and seems to work reasonably well
ADD COMMENT • link written 3.6 years ago by Mark Crowe • 100
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