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Created 2014-07-10 18:31:00 | Updated | Tags: haplotypecaller reads snps forward reverse
Comments (3)

I don't see any information from this post http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk,

I was wondering if it's possible to get the number of forward/reverse reads in the final VCF outputted by HaplotypeCaller?


Created 2012-11-29 08:16:23 | Updated | Tags: bam walker summary mapping reads
Comments (4)

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