How to Read Alleles in Samtools

Question

[noob@bioinfo]

Hello,

I'm quite new at using Samtools and figuring my way around it. I am looking for SNPs for some disorders, and I got the following output:

2   #position   G   8   .a,...,.    ]]]]]]]]    FFFFFFFF

I understood that the 5th column tells me whether . or , means a base matching to the reference base on the forward or reverse strand. Does this mean all the reads having stops (.) are G, and hence all commas(,) are C? Is there a way to see the actual alleles obtained in these reads?

Thanks a lot!!

Answer 1

[Brice Sarver]

Check out the manual page of samtools mpileup.

It may be easier to use samtools view to subset on positions of interest and explore those to see what's going on to convince yourself that you're looking at the right things. Also, check out IGV for a nice way to visualize BAMs.