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uclahs-cds / pipeline-call-sSNV

A Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.
https://uclahs-cds.github.io/pipeline-call-sSNV/
GNU General Public License v2.0
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Additional Benchmarking to be added to README? #285

Open sorelfitzgibbon opened 7 months ago

sorelfitzgibbon commented 7 months ago

/hot/user/sfitzgibbon/PCAWG-63/benchmark-call-ssnv

Input was 30 tumor/normal pairs from the PCAWG-63 dataset, chosen because they had complete pipeline-call-sSNV results. Default v8.0.0 F72.config resources were used.

Sample IDs:

Nextflow trace files:

Per sample mean coverage:

Sample coverage

type min max average
tumor 24x 71x 44x
normal 24x 50x 32x

Runtimes per sample (summed over parallel jobs)

Tool min max average
MuSe 1h 54m 4h 40m 3h 6m
Mutect2 68h 10m
SomaticSniper 13h 15m
Strelka2 5h 30m

Cpus per sample

Tool min max average
MuSe 1174% 1191% 1185%
Mutect2 4733%
SomaticSniper 291%
Strelka2 1121%

CPUhours

Tool average
MuSe
Mutect2
SomaticSniper
Strelka2

Memory (max rss)

Tool min max average
MuSe 33.3 GB 46.8 GB 39.1 GB
Mutect2 27.7 GB
SomaticSniper 4.41 GB
Strelka2 3.32 GB
sorelfitzgibbon commented 7 months ago

Had mistakes, will repost later