Christoffer Flensburg

Hi Lisle! I am also having issues with running out of memory after a few hours. I am running on three human exomes with: ``` java -jar abra2-master/temp/abra-0.94c.jar --in cancer1.bam,normal.bam,cancer2.bam...

Eww, i just saw a .jar and used that one, didn't realise it was super old, sorry about that. 😬 I ran with the latest release, and it works fine...

Hey! That part is where the reference normal BAM files are identified. I think it doesn't find any BAM files. I really thought it'd make a more informative error message...

Hey Michael! SuperFreq calls absolute copy numbers, so without copy number alterations in the sample, it should call 1 copy of X and 1 copy of Y for a male,...

Hey! SuperFreq re-normalises the reference normals to diploid which the studied samples are then compared against. So superFreq mislabeling female samples as male, will incorrectly double the chrX counts used...

Hi! Happy to hear the package is seeing some use! It's a reasonable request to plot only one panel, and indeed we often end up making plots of only read...

Hey! The logic is valid. I think sample and sample.1 are the clonalities (note sample cell fraction, not cancer cell fraction) of the variant in the samples. The river output...

SuperFreq needs samtools to be available through a `system("samtools --version")` call from R, and from the warning that doesn't seem to be the case. Docker and conda are out of...

Hey! superFreq tells featurecounts to not use the paired end information when running in genome mode, because featurecounts resorts the bam file to have the pairs next to each other....

Ok, I had a closer look at the latest Rsubread version, and they have indeed changed syntax for how to tell it to to count raw reads (not fragments) in...