Hi, I phase read alignments using `samtools phase`. How can I get the
phased VCF from phased BAM files? Is it possible to do at the command line?
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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
On Thu, Apr 20, 2017 at 03:52:11PM +0900, kenichi chiba wrote:
> I would like to ask for help about samtools mpileup. The output of
> samtools mpileup may differ depending on the presence or absence of the
> -f option. If there are probably about 20 bp deletions, some deletions
> are missing
Hello,
I would like to ask for help about samtools mpileup. The output of
samtools mpileup may differ depending on the presence or absence of the
-f option. If there are probably about 20 bp deletions, some deletions
are missing from the output.
$ samtools --version
samtools 1.2
Using htslib
