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Old 06-23-2015, 11:12 AM   #1
Location: OP Kansas

Join Date: Mar 2014
Posts: 53
Question SNP calls with IGV

Good day all!

I have a quick question about SNP calls, more of a best practice I suppose. For my project we are using single end Ion Torrent PGM data for WGS of infectious bronchitis virus. It is a +ssRNA virus so we used the RNAseq pipeline for library prep. The sequenced was aligned to the NCBI RefSeq for IBV using TMAP. In the attached file at 19,095 and 19097 there are two SNPs that are linked. i.e. if its A at 19095 its G at 19097, similarly if its C its T in the other.

The reads are sorted by map quality so the reads at the top are the best mapped to the reference, and when I make the call in the draft I will make the corresponding call as well, but how do you make this call?
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File Type: png SNPs.png (30.7 KB, 22 views)
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