facets-suite
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mskcc
Utility functions for FACETS
Hello, I would like to ask what would be the recommended cval number for WES data with 40x coverage when using facets-suite? I come across this post (https://github.com/taylor-lab/facets-suite/wiki/1.-Running-FACETS) and would...
Dear all, I get this error with > ccf_annotate_maf(mafFile). > "Columns t_alt_count and t_depth required" When I import the maf files to maftools, I can see both of them under...
Current version(v2.0.8) initialize "--purity-cval" as integer 100, and argparse parse this argument as integer, too. One couldn't set "args$purity_cval" as NULL when only running one-pass .
Recently I used this pipeline in docker. It's very convenient to generate downstream outputs, thanks! However, I encountered some issues during the analysis. 1. Error when running `snp-pileup` binary ```...
https://github.com/mskcc/facets-suite/blob/41a01fe9afb947f38af2802cf62189e0a1061cc5/R/ccf-annotate-maf.R#L58 Here, we overwrite the true read depth with alt+ref. Normally, this doesn't change much but I've seen positions where there are 3 alleles present at a given position and...
The fraction_loh from copy-number-scores.R is wrong, while the rac_loh from check-fit.R is correct. The line 92 of copy-number-scores.R should be changed: "loh = as.numeric(sum(length[lcn == 0]))“ change to "loh =...
Hi, There is a minor error here: https://github.com/mskcc/facets-suite/blob/master/R/ccf-annotate-maf.R#L29. The check is for the presence of `t_alt_count` and `t_ref_count` columns, but the error message is "Columns `t_alt_count` and `t_depth` required." Also,...
Hi all, First of all, thank you for this tool, we found it very useful for our samples! I had a interpretation question from the facets output columns tcn.em and...
Hi, I am using FACETS Suite to call somatic copy number changes from whole exome seq data. I combined all the gene_level.txt files into one for all samples to summarise...
The `run-facets-wrapper.R` script requires tumor-normal output from snp-pileup. However, the script does not seem to offer any way to record the ID for the tumor and normal samples. It has...
