PureCN: Tool for estimation of tumor purity and ploidy

Question

[sruthi]

Hi, I'm trying to calculate tumor purity and ploidy using a tool called PureCN written in Rscript. The initial step is to generate an interval file based on GC content from hg38.bed and hg38.fa files. The command used for the process is given below: Rscript $PURECN/IntervalFile.R --infile /path/to/hg19.bed --fasta /path/to/hg19.fa --outfile /path/to/hg19_intervals.txt

The following error shows up:

Error in value[3L] : record 4423505 (chr1_KN196472v1_fix:111333-111727) failed file: /path/to/hg38.fa Calls: preprocessIntervals ... tryCatch -> tryCatchList -> tryCatchOne -> <anonymous>

It would be of great help if someone could help me out in troubleshooting this error. Thanks in advance.

Answer 1

[markus.riester]

Hi,

the infile needs to be a BED file with the capture baits. This file should only contain regular chromosomes. If it does, please open a GitHub issue at https://github.com/lima1/PureCN/issues, ideally including a minimal BED file to reproduce the issue.

Thanks a lot, Markus

[sruthi]

Thanks Markus. I uploaded a BED file with capture baits, but the same error pops up. Is there something that I must look in the FASTA file? Also, which build is supported by the tool? hg19 or hg38.

[markus.riester]

Both builds are supported. Please try to create a reproducible example, like a minimal BED file and open an GitHub issue. Thank you.

[sruthi]

Thanks Markus. I will open an GitHub issue.