find all alleles mutated with depth X20

Question

[sahar850]

Hi,

I'm new to the subject. I got a sam file and fasta file, I need to get all the allele ref = G alter = T with a specific depth. As I understand it I need to use samtools, but I never worked with it..can anyone get me in the right direction?

[Pierre Lindenbaum]

http://www.htslib.org/workflow/

[lakhujanivijay]

Hi sahar850

Since you are new to this subject (and thanks for letting us know that), you must first perform what is known as "variant calling". After that you will get a VCF file and then you can apply the depth based filters for .e.g see this post:

Filter SNPs on depth

Since you haven't mentioned any background information about your data, I am afraid if anyone would be interested in pointing you towards the right direction. Please see the below posts and reframe or re-write your question

How To Ask Good Questions On Technical And Scientific Forums

Brief Reminder On How To Ask A Good Question