Extract Reads with Allele Type in IGV

Question

[selplat21]

I have aligned reads to a genomic sequence for which there is a clear SNP. I have grouped alignments based on this SNP, which gives me a set of reads with a T at this site and a set of reads with a C at this site. Is there a way to either extract only reads with a particular allele OR get a consensus sequence for one of these read types?

Answer 1

[Pierre Lindenbaum]

How to extract reads with a known variant form a bam file

how to extract allele specific reads from bamfiles?

Extract reads with variant at given position

[selplat21]

Thank you!