Dear all,
after installing samtools 1.13 (using htslib 1.13), I saw from the samtools
depth usage message that there is multi-threading option "-@ INT" for samtools
depth.
I tried the following command to test this option.
samtools depth -@ 7 -a -b panel.bed sample_sorted.bam > output.txt
It worked fine, but I saw no acceleration when compared to omitting "-@ 7".
Likewise, top indicated usage of just one CPU.
I accidentally omitted the INT subsequent to -@, leading to the following
command.
samtools depth -@ -a -b panel.bed sample_sorted.bam > output.txt
This resulted in a substantial acceleration, while the result file was
identical to the previous call.
Should I better use the multi-threading option of samtools depth without
indicating the number of intended threads/CPUs?
BTW, when I tried to consult the man page of samtools depth ("man samtools
depth"), I unfortunately found no information regarding the multithreading
option.
Best regards
Frank
Dr. rer. nat. Frank Vorhölter
Leitung Bioinformatik
Überörtliche Berufsausübungsgemeinschaft - GbR
MVZ Dr. Eberhard & Partner Dortmund
Brauhausstraße 4
44137 Dortmund
Tel.: +49 231 9572 6612
Mail: [email protected]<mailto:[email protected]>
Web: www.medizin-zentrum-dortmund.de<http://www.medizin-zentrum-dortmund.de/>
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