Hi GATK Team! I was wondering if there is a way to get Haplotype Caller in ERC BP Resolution mode to emit details for every base for every position? That is, for each position rather than just emitting in the ALT column, or in some cases an alternate allele or multiple alternate alleles and , is it possible to get it to emit every single base that had support in any of the reads - that is, samtoolsmpileup-like information where for every position there is information on the number of reads for A/C/T/G?
In particular, I am hoping to do this for a given set of positions I am interested in - would be great if there is an option for this as well.
I was hoping to potentially use this rather than an mpileup since local reassembly is performed on these sites.
Thanks a lot!
Alon
