search

etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
Other
520 stars 163 forks source link

how long will cnvkit run a case? #674

Closed xinmiaoyan closed 2 years ago

xinmiaoyan commented 2 years ago

hi ,nice tool. I've run CNVkit to call CNVkit alteration on WES data, and it took a long time and didn't have any updates in 4 hours, is there any thing wrong or it does need a lot of time. Code is below and get some updates in the beginning. appreciate your response.

cnvkit.py batch B485700.sorted.bam\
                  --normal n485700.sorted.bam \
                 --targets access.hg38.bed \
                --fasta hg38.fa \
               --access access.hg38.bed \
               --annotate refFlat.txt \
               --output-reference my_reference.cnn \
               --output-dir B485700_C485700
CNVkit 0.9.6
Detected file format: bed
Splitting large targets
Applying annotations as target names
Detected file format: refflat