Thank you very much. Now I understand well. If the -B option is
specified, the missing deletion will be output. When the -f option is
not specified, mpileup is handled as -B Disable BAQ calculation.
Best regards,
Ken
On 2017/04/20 17:15, Federico Abascal wrote:
I asked this sometime ago… The
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 coverag
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 fro
On Fri, Feb 20, 2015 at 6:36 PM, David Francisco
wrote:
> Hello
> I'm using samtools version 1.1 and every time I give the folowing command:
>
> samtools mpileup -C 50 -ug -f PSP/data/hg19/hg19.fa
> PSP/data/PSP10/PSP10.recal.bam > PSP/data/PSP10/PSP10_sam.bcf
>
> I get the following message:
>
>
