Dear samtools-help list,
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.:
samtools mpileup -L 999999999 -d 999999999 -r chr1:50000001-50025000 -b
BAM.list --fasta-ref REF.fasta -a -a -t AD,DP -Q 0
Thsi should result in 25000 sites, however the number is lower.
Has somebody stumbled about the same problem and might have a solution.
Actually the number of sites even drops if I am using the '-I' option.
Best regards and thank you in anticipation
--
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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