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pughlab / bamgineer

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
Apache License 2.0
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Missing chromosomes? #14

Open MaxSalm opened 4 years ago

MaxSalm commented 4 years ago

Hi there, thank you for this initiative, it is vital for the community. I have run into a problem. I tried to simulate a very simple situation (loss of chr3 & chr8, gain of chr4 & chr9). Rudimentary logR analyis shows the events have been engineered into the target BAM. However, chr10 and chr15-22 also appear to have been lost ...

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All ideas welcome!

MaxSalm commented 4 years ago

Is this to do with chromosome ordering by any chance?

suluxan commented 3 years ago

Hey Max,

Sorry for the late reply, was there any update on this? Were chr 10 and 15-22 included in the input bam files?