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KCCG / ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
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No dots/lines in the coverage by chromosome view (CBCV) #60

Open Bin-Guan opened 5 months ago

Bin-Guan commented 5 months ago

Hello, We run version 1.1 on a bam and all steps completed without errors. However, the coverage by chromosome view in the QC_report.pdf showed 24 lines of "## Warning: NAs introduced by coercion" followed by a grid of 1 to 22 without dots or lines. What could be the problem?

Tested using the supplied bam file NA12878.grch38.subsampled.bam, it showed the same problem. The text file in SVs\qc\chromView\ only had chromosome numbers but no other information: chr1 TAB ... chrXX TAB chrY0 TAB chrM TAB

Thank you.

Bin-Guan commented 5 months ago

Here is the pdf report, where the other plots were fine except the CBCV. COL005.1.QC_report.pdf

J-Bradlee commented 2 months ago

Hi @Bin-Guan thank you for bringing this up. I get the same results. I think it has something to do with scripts/validReportPrep.pl line 256-264 on the v1.1-dev branch. Working on it!