[Samtools-help] Is there a way how I can figure out how many reads have been removed by applying rmdup?

Is there a way how I can figure out how many reads have been removed by applying rmdup? I have a file foobar.bam containing paired-end reads, and I want to remove PCR duplicates, and also I want to know how many pairs have been removed. Here is what I am doing at the moment: # sort foobar.bam sam

Re: [Samtools-help] BCF2.2 and VCF version interop

Hi Chris, yes, that is correct. BCF can contain different VCF versions Petr On Mon, 2017-02-27 at 12:06 -0500, Chris Norman wrote: > I'm not sure if this is a spec or implementation question, but I'd > like to verify that the BCF version of a bcf file, and the embedded > VCF header/version, are