find all alleles mutated with depth X20
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?
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sahar850 •
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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