Comments (4)
Hi Kun,
thanks for the message!
You are right, samtools
should be $samtools
.
but luckily, whenever we are in the mitozEnv
environment, both samtools
and $samtools
will work.
from mitoz.
Yeah, but samtools print help massage and pipeline stopped somtimes, and every thing goes well when I change samtools to $samtools
Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]
Options: -b output BAM
-h print header for the SAM output
-H print header only (no alignments)
-S input is SAM
-u uncompressed BAM output (force -b)
-1 fast compression (force -b)
-x output FLAG in HEX (samtools-C specific)
-X output FLAG in string (samtools-C specific)
-c print only the count of matching records
-B collapse the backward CIGAR operation
-@ INT number of BAM compression threads [0]
-L FILE output alignments overlapping the input BED FILE [null]
-t FILE list of reference names and lengths (force -S) [null]
-T FILE reference sequence file (force -S) [null]
-o FILE output file name [stdout]
-R FILE list of read groups to be outputted [null]
-f INT required flag, 0 for unset [0]
-F INT filtering flag, 0 for unset [0]
-q INT minimum mapping quality [0]
-l STR only output reads in library STR [null]
-r STR only output reads in read group STR [null]
-s FLOAT fraction of templates to subsample; integer part as seed [-1]
-? longer help
from mitoz.
Hi Kun,
Agree, $samtools
will always work.
Could you please indicate when samtools
alone doesn't work? Like when submitting the job to an SGE cluster to run? I am just curious about it, I will change the code to $samtools
in later releases. Maybe in some situations when executing the above commands the current environmental variables (i.e., $PATH
) were not inherited.
from mitoz.
See https://github.com/linzhi2013/MitoZ/releases/tag/3.5
from mitoz.
Related Issues (20)
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from mitoz.