GATK4 ASEReadCounter Function of VCF

Question

[hgal4248]

Hi all,

I am using GATK4 ASEReadCounter to create the inputs for an ASE analysis.

I understand that the inputs are pre-processed + mapped .bams, reference genome and a VCF for specific sites to be processed (As per GATK documentation).

I was wondering what the full function of the VCF file is in this program. Is ASEReadCounter solely using the vcf to determine which sites in the .bam to count or does it play other roles in the process that contributes to the output counts.

Any information would be amazingly helpful, thank you.

Answer 1

[geocarvalho]

Hi, I'd recommend reading the paper "Tools and best practices for data processing in allelic expression analysis" suggested in the GATK ASEReadCounter website where it says:

...an easy to use tool in the widely used GATK v.3.4 [23, 24] called ASEReadCounter, which does not require any additional setup, and includes a variety of easily customizable read processing options as well as professional maintenance and documentation, similar to other GATK tools. Both operate on aligned RNA-seq reads and count the reference and alternative allele reads that passed filters for mapping and base quality at each bi-allelic heterozygous variant. The GATK tool offers several additional options for processing RNA-seq reads: by default each read fragment is counted only once if the base calls are consistent at the site of interest, and duplicate reads are filtered (see below). Other options allow filtering for coverage and for sites or reads with deletions...

Maybe you can find more information in the references of this paper.