See option -d, --max-depth. Also -F, -L, -m for indel calling.
These count all reads overlapping a candidate variant site, rather
than by starting position.
- tom blackwell -
On Mon, 1 Feb 2016, G�nter J�ger wrote:
Dear Samtools-Team,
I encountered that samtools mpileup followed by bcftools for variant
calling produces different results when the bam file is sorted
differently. Since the bam file has to be sorted by coordinate, the
order of reads sharing the same start position may vary in different
versions of the bam file, i.e. if reads in a coordinate sorted bam file
are shuffled and then sorted by coordinate again, the order of reads
mapping to identical start positions usually differs from the order of
the same reads in the initial bam file.
This however, does change the quality of the variants that are called by
bcftools. Is suspect that the genotype likelihoods change. I would have
expected that changing the order of reads mapping to the same start
position does not influence the variant calling, when using the exactly
same samtools mpileup/bcftools commands. I use the current version 1.3.,
but also older versions show that problem.
Is there any explanation why this is the case? The problem occurs with
every bam file I tested so far. It seems like samtools mpileup does not
use all of the reads overlapping a variant position for likelihood
estimation?! Is there any option in bcftools or samtools mpileup to
prevent this from happening, i.e. to produce the same variant quality
scores/genotype likelihood values regardless of the order of reads?
I would appreciate any comments on that.
Best regards,
Günter
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