Hi, Does GATK2 provide a walker/option to summarize the read alignment in a given BAM file? The summary including total reads, reads mapped/%, reads uniquely mapped/%, reads uniquely mapped with 0mm/%, reads mapped on-target/%, reads uniquely mapped on-target%, etc is of great use to assess the mapping quality for whole genome or targeted analysis. Please advice me on how I can obtain this using any of the walkers available. Thanks, Raj
Hello GATK Team,
there are currently two walkers for phasing in the GATK PhaseByTransmission and ReadBackedPhasing. Because of their different information source (PhaseByTransmission has the called VCF file, ReadBackedPhasing the BAM files) these can produce different or complementary genotypes. There used to be a walker for this job "MergeAndMatchHaplotypes" but it seems to be discontinued.
What is the current recommendation for Trios? Only use PhaseByTransmission?