Christoffer Flensburg

Probably? You'd need to convert the data to whatever format they want, but the information should be there.

Hi! That error message is not very informative unfortunately. I'd have to look at the logfile (located in the Rdirectory R/myIndividual/runtimeTracking.log) for clues. Maybe also let me know which version...

Hi! Yep, the CNVsegment file is a recurring question so I finally made my first entry in the wiki! [https://github.com/ChristofferFlensburg/superFreq/wiki](https://github.com/ChristofferFlensburg/superFreq/wiki) For variants, "var" is number of variant supporting reads (ref...

Hmm, yeah memory really shouldn't be an issue in that part of a pipeline. You're correct that the variants are not yet read in to memory at that point, and...

Thanks Jake. It does indeed solve the issue with the empty first page, but it doesn't allow you to output multipage pdf. In my case I only wanted a single...

I haven't had this issue in base plotting. After a quick google, it seems like an issue with ggplot and pdf(): https://github.com/wilkelab/cowplot/issues/24 According to Claus Wilke in that thread, ggsave()...

Hi! The ploidy isn't output explicitly, but it's easy enough to calculate from the segments, just the average copy number (so 2*2^M) over the segments, weighted by segment size (x2-x1)....

If you have only females, then you lose the ability to find recurring noise on chrY, but people typically don't care about chrY mutations, so probably not an issue. Perhaps...

hi! The dots in the top panel are essentially log fold change of (library normalised) counts between the studied sample and the reference normals. The wide spread in your data...

The copy number calls are in plots/myIndividual/data/CNAsegments_mySample.tsv.