How can I obtain genotypes from .bams of RNAseq data?

Question

[hgal4248]

Hi all,

I am hoping to run an allele specific expression analysis on a set of RNAseq samples I have. I need to obtain the genotypes for all samples to determine heterozygosity of each variant which is needed for my final analysis.

How can I obtain the variant genotypes per sampple?

I have tried GATK HaplotypeCaller on my filtered .bams however this takes an immense amount of time on the HPC I have access to. Is there another method besides variant calling that can produce genotypes, or any way reduce the compute time for the variant calling.

Any help would be immensly appreciated.

Note: I am new to this kind of analysis, so please excuse my lack of knowledge of some terminology.

[4galaxy77]

You kind of have to do the time-consuming genotype calling step to obtain genotypes from a bam file. The .bam doesn't contain genotype information, only read information.

Answer 1

[Istvan Albert]

If you know what variants you are looking for it is possible to genotype without aligning the reads, look for tools like those described in the paper below:

FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads

https://www.nature.com/articles/s41598-017-02487-5