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Old 03-04-2014, 11:40 AM   #1
Avro1986
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Location: Montreal

Join Date: Dec 2012
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Default Problem retrieving snps and indels from FVB mouse

Hi everyone!

I am looking at co-occurring events in transgenic FVB mice tumours. First, I need to filter out snps and indels. I was reading the following paper: Sequencing and characterization of the FVB/NJ mouse genome by Wong et al. 2012. The research group has identified snps and indels in the FVB with next-gen sequencing. I am trying to retrieve this data that is stored in a huge vcf file at the Wellcome Trust Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/).

The file is huge and contains the genetic information of 18 different mouse strains (including FVB). I downloaded tabix/cvftools and installed their binaries to my PATH. My problem is that I don't know how to extract the SNP/indel coordinates (and what they are) from this file. I have already spent quite some time reading the documentation and googling, but I am stuck.

Has anyone done something similar? I would greatly appreciate if someone could please give me some hints.

Thank you!
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