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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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Genotype info missing for X and Y chromosomes #76

Open popicka opened 4 years ago

popicka commented 4 years ago

Hello,

Sometimes information for predicted LOH calls is missing in the outputs which causes the assess_significance.R function to fail. This happens for chromosomes X and Y.

Here is an example of the error reported: Loading required package: GenomeInfoDb Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 911 did not have 9 elements

This is an example of the row: X 155700000 156040895 0 loss somatic 0

Do you maybe know what is causing this problem?

Thank you for this great tool, Ana

valeu commented 3 years ago

Dear Ana, yes, it looks like it happens specifically for X and Y. Will be changed in v11.7.