SNP calls with IGV

[skbrimer]

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?

[Jessica_L]

I'm slowly picking up more data analysis and bioinformatics at work, so I've been doing some of the same kind of work lately. Here's how I would look at that:

I see 11 of the A and G reads, 9 of the C and T reads (along with some sequencing errors that are too probably too hard to call). Based on experience with Sanger data, it looks like a heterozygote, but IGV doesn't (as far as I know) really make it easy to see total read depth. To make that call, I'd look at something like the vcf file and check out the allele depth at the indicated SNPs to see how many reads you have of each genotype.

Since I'm still new at this, I'd be interested to see how others would analyze similar data.

[skbrimer]

Thank you Jessica, that is a good suggestion. I will give it a try and see if it does shake out for me.