Comments (3)
Actually, could it be because make
(now?) runs make all
?
from cnvkit.
It's definitely an outdated benchmark -- I've added a few more samples to process since then and also generate "diagram" and "scatter" plots for every sample now. More importantly, I usually run make -j
to parallelize it, and on an 8-core Linux workstation that does finish in about a minute. I just timed it on my laptop: 6 minutes, 3 seconds.
The README also mentions "TR" and "EX" datasets which I moved to another repo: https://github.com/etal/cnvkit-examples
I'll update the sentence to "a few minutes", mention the -j
flag and link to cnvkit-examples.
from cnvkit.
Fixed here: 1af29df
Let me know if this still looks unclear or misleading.
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Related Issues (20)
- Installation error HOT 7
- Unable to produce .cnr files HOT 2
- Getting BAF and allelic imbalance in export vcf
- Improper post-processing of segment [bug]
- Unable to use fix without antitarget file for WGS samples
- Merging segments while running pipeline
- `segment` function fails HOT 1
- Somatic CNV calling in case of pre-existing CNVs
- Installation problems HOT 5
- Unable to load BED file with skgenome
- cnvkit.py segment error
- CNVkit segment command RuntimeError: Subprocess command failed HOT 1
- access command: recommended -s (mingap) value
- Blank plots HOT 1
- Possible bug in bin sizes
- segment with cbs method - threshold
- call with filters cn, ci, sem
- Filtering single-cell false positive calls
- targeted DNA seq
- Proper read pairs
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