View Single Post
Old 11-04-2013, 01:51 PM   #1
rzeng
Member
 
Location: houston

Join Date: Aug 2013
Posts: 19
Default variant filtering of mouse whole exome sequencing

hi, I have general question here about exome sequencing variant filtering.
I have generated mouse exome variants data from several samples using my pipeline including BWA alignment, samtools, picard and then GTAK. Also i got variant annotation table using Annovar.

However, I was struck here since I have biology background with not computer program skills before. First I need to filter variants by using public resource dbsnp or variant data. I have downloaded variant data from Sanger which has variants callings from 17 mouses. however, i do not know how to start to filter these data using it. I have tried with Annovar variant_deduction.pl but it did not work on non-human data.

Second, I have variant data from several different samples but how i use these data to filter variants? Is there good open resource that I just need to input my variant data and it can help me to filter these data?

http://doc.goldenhelix.com/SVS/latest/index.html

I found this SNP & Variation Suite from Golden Helix website. Anyone has used it and if it works just for human data too?

Thanks

Last edited by rzeng; 11-04-2013 at 01:56 PM.
rzeng is offline   Reply With Quote