Dear Samtools team,
The samtools depth command sets a max depth of 8000 to the aligned reads.
Previously the max threshold of 8000 was replaced by adding the
bam_mplp_set_maxcnt(mplp, 1000000)
line in the "bam2depth.c" file.
In the 1.3.1 release of Samtools this has been corrected, and "bam2depth.c"
already contains the following lines:
if (0 < max_depth)
bam_mplp_set_maxcnt(mplp,max_depth);
The max_depth is set with the -d option of the mpileup command.
Is there also a way to specify the max_depth for the depth command?
Thanks,
Lilit
--
Lilit Nersisyan
Junior Researcher, MSc
Institute of Molecular Biology NAS RA
7, Hasratyan str., 0014, Yerevan, Armenia
Tel.: +37494 601703, +37410 282622
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