Re: [Samtools-help] bug in samtools mpileup?

tive BAQ > calculation with -E. I’ve heard that the latter option will be turned on by > default in the next version of SAMtools. > > Try option --no-BAQ on the pileup with a reference. > > Colin > > On 17 June 2016 at 06:22, Federico Abascal <f...@sanger.ac.uk > <mail

[Samtools-help] Extended BAQ

Hi all, Is the Extended BAQ calculation the default when invoking samtools mpileup? For samtools calmd there is an option “-E” that enables the extended BAQ calculation, but there is no such option for mpileup and I read somewhere that the extended calculation would become the default. Many

Re: [Samtools-help] problem with samtools mpileup

I asked this sometime ago… The reason is because when you provide the fasta reference file, then BAQ is enabled. BAQ does realignment and base quality score recalibration and results in different mpileup outputs. In my experience BAQ is very good at removing false positives, but when the