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broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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Fail to plot analysis for only one chr #57

Closed mpierrejean closed 5 years ago

mpierrejean commented 5 years ago

It seems that the plotting function doest not work with only one chromosome is provided. Line 348 in plotting function.

Could you test if the length of the chromosome list is equal to one?

Thanks

gavinha commented 5 years ago

Hi @mpierrejean

For plotting one chromosome, it shouldn't be invoking getGenomeWidePositions(). Can you please let me know how you're trying to plot one chromosome and which functions you are using to do this? This will help me figure out why you're running to this issue.

Thanks, Gavin

mpierrejean commented 5 years ago

Hi @gavinha

I have the following error:

Error in chrBkpt[i] <- prevChrPos : replacement has length zero Calls: plotGWSolution -> plotCNlogRByChr -> getGenomeWidePositions

We performed tests on short bam files to create a pipeline with ichorCNA. The bam files only contain the chr20. 

ichorCNA.sh \
    -f "${TEST_DIR}/conf.txt" \
    -ctrl "${TEST_DIR}/control.bam" \
    -o "${TEST_DIR}/result" \
    -chr 'chr20'

In conf.txt there is one line CRPC1=tests/test1.bam,tests/test2.bam

ichorCNA.sh calls the function runIchorCNA.R in ichorCNA/scripts/ichorCNA/scripts/runIchorCNA.R.

I hope I gave enough details. I will not available for the next 4 weeks.

Thanks.