Help with SNP counting

Question

[ofer.aidlinhara]

Hey all,

I can really use your help here,

I working on a non-model organism and I mapped Illumina trimmed reads, using Bowtie, to a specific locus which I've built index for. My goal is to be able to say for certain positions of interest, how much reads contained each nucleotide (for example, position 211 - A 2/100 G 12/100 T 40/111 C 46/100). I started with Free Bayes but I can't find in the output this kind of information. 1) do you if I can get this information from Free Bayes? and how? 2) do you have recommendations for another procedure?

Thanks Ofer

[ofer.aidlinhara]

Thanks JC, I'll take a look at it.

[ATpoint]

Always align against the full genome. Partial/selected references out of the full reference will attract false alignments as the true origin of a read might be missing but the aligner will still try to match every read to the best fit in the existing reference.

Answer 1

[JC]

FreeBayes VCF will output only variant positions, if you want to check other regions, samtool mpileup function could be more informative