Filter reads by SNP by genotype

Question

[katrina.eaton]

I am trying to filter files by the specific genotype at a specific SNP. Example: I want all the reads with a "T" in position chr1:181188090. Everything I've seen so far is looking at the quality of the reads, but that's already been addressed.

This can't be that difficult, clearly I'm missing something, but I don't know what. Any help would be greatly appreciated.

[GenoMax]

Assuming you have the BAM file you could extract all reads that overlap an interval that contains that SNP and then filter for the specific position. e.g. Extract Reads From A Bam File That Fall Within A Given Region and extract reads from BAM whose fragments overlap a specified region

[katrina.eaton]

I have a bam file that has all the reads that overlap the interval in question, the part I can't figure out is how to filter for only the reads that have a T at that position.

To elaborate: I'm looking at a maternal plasma sample, and am trying to isolate the fetal fraction. I have SNPs where I know what the genotype is, and the fetus has one allele different from the mother. I'm trying to isolate the fetal reads, to then determine the read length.

The filtration examples I've seen have been for quality or some other metric, I'm struggling to find a way to get a stream of nucleotides from that one position to filter.

Answer 1

[GenoMax]

How about @Pierre's solution here: How to extract reads with a known variant form a bam file

[katrina.eaton]

This looks great! I will try that. Thank you very much!