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berman-lab / ymap

YMAP - Yeast Mapping Analysis Pipeline : An online pipeline for the analysis of yeast genomic datasets.
MIT License
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Upgrade samtools to allow parallelization #36

Closed vladimirg closed 8 years ago

vladimirg commented 8 years ago

Our current version of samtools (0.1.18) doesn't support parallelization, but the recent version (1.3.1) does (the -@ flag for the view and sort commands). The output formats should remain the same, but parameters given to samtools might have changed since then. Worth an investigation - can shave off some time off the processing.

Requires #32 .

vladimirg commented 8 years ago

Parallelizing mpileup is possible by running parallel instances of mpileup on different regions (https://www.biostars.org/p/48781/). We could run it per chromosome, as there are usually more chromosomes than cores anyway, making sure that at any given moment the number of running mpileup instances is the number of available cores.