PureCN
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lima1
Copy number calling and variant classification using targeted short read sequencing
**Describe the issue** When I run PureCN on 10 tumor samples and use their paired 10 germline samples to create a reference, I get different cellularity and ploidy results from...
**Describe the issue** A error had happened whenI'm running PureCN.R. **To Reproduce** FATAL [2022-08-04 15:23:30] f not in expected range. FATAL [2022-08-04 15:23:30] FATAL [2022-08-04 15:23:30] This is most likely...
**Describe the issue** When NAs are found in the BQ field `.readAndCheckVcf` crashes when trying to log a warning. The following if-statement is the culprit, since `n` is never defined:...
Hi, I am trying to run Coverage.R from the latest Purecn docker. The command that I am running is ``` Rscript $PURECN/Coverage.R --out-dir normaldb/ --bam bam.list --intervals xgen-exome-research-panel-probesbe255a1532796e2eaa53ff00001c1b3c.hg38.bed.gz --cores 30...
Hi Markus, More of a general question - I was wondering if purecn would eventually be CRAM compatible? Thank you!
Hi, I would like to know why arbitrary thresholds of 6/7 were selected to label amplifications - was an internal comparison performed to define these thresholds? Is it safe to...
Question
Hi, May I ask you for some advice, in cases when I see that the selected model by pureCN is off e.g, lower purity than expected or mutations expected to...
- [ ] gene-level summary not necessarily best way of doing it. check if we can safely extend to neighboring baits. maybe start 500kb left and right, iteratively shorten to...
Latest versions seem to have reduced artifacts quite a bit, but some are very difficult to get rid off. Flag genes with GC-content outliers, low mappability, small number of targets...
Probably wrapper around https://github.com/sztup/scarHRD