variant calling for specific genes/chromosomal locations

[debarka]

Friends:

I need to use GATK for variant calling from single cell RNAseq data for huge number of cells. Therefore, I need to narrow down my search. I would like to specify chromosomal locations or gene names for which I am interested in variant calling.

Can somebody tell me how to do that?


Debarka

[Brian Bushnell]

The best way would be to filter for only the reads that mapped to those locations, removing everything else, then do variant calling. If you know the coordinates, just write a program that parses the sam file, which is not too difficult.

[debarka]

I think you are right. actually SAMtools allows specifying chromosomal locations.