It seems that if I use this here:
'samtools mpileup -L 999999999 -d 999999999 -r chr1:50000001-50025000
--fasta-ref REF.fasta -a -a -t AD,DP -Q 0 -A -B -b BAM.list'
I get the correct number of lines
HOWEVER, if I add the options '-u -v' so that the output should be
uncompressed and in VCF format, than the output has duplicated POSITIONs
and in total less than the expected 25000 sites, if I remove the
duplicated. So there might be an issue in reporting the VCF output or in
translating the compressed to uncompressed output.
See commands attached:
samtools mpileup -L 999999999 -d 999999999 -r chr1:50000001-50025000
--fasta-ref REF.fasta -a -a -t AD,DP -Q 0 -A -B -u -v -b BAM.list | awk
'{if(substr($1,1,1)!="#") print $2}' | sort | uniq | wc -l
[mpileup] 6 samples in 6 input files
(mpileup) Max depth is above 1M. Potential memory hog!
24923
and without the '-u -v'
samtools mpileup -L 999999999 -d 999999999 -r chr1:50000001-50025000
--fasta-ref REF.fasta -a -a -t AD,DP -Q 0 -A -B -b BAM.list | awk
'{if(substr($1,1,1)!="#") print $2}' | sort | uniq | wc -l
[mpileup] 6 samples in 6 input files
(mpileup) Max depth is above 1M. Potential memory hog!
25000
Best regards
Kristian
On 07/12/2017 05:46 PM, James Bonfield wrote:
On Wed, Jul 12, 2017 at 04:41:17PM +0200, Kristian Ullrich wrote:
whatever I am doing with both 'samtools mpileup' and 'bcftools
mpileup', in both cases not all sites are reported, even if I
specify the '-a -a' options e.g.:
My standard first try at explaining anything odd with mpileup is to
test it with (default) and without (-B) the BAQ calculation. Also
consider -A too.
Does adding -B change things for you? (If it does, explaining why and
deciding if it is an improvement is a totally different and more
complex issue!)
James
--
Kristian Ullrich, Ph.D.
Department of Evolutionary Genetics
Max Planck Institute for Evolutionary Biology
August Thienemann Str. 2
24306 Ploen
Germany
+49 4522 763 274
ullr...@evolbio.mpg.de
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