The analysis workflow consists of 2 tasks: GC-content bias correction (using HMMcopy) a. Computing read coverage from ULP-WGS b. Data correction and normalization CNA …

May 12, 2019 · Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing. - broadinstitute/ichorCNA

The analysis workflow consists of 2 tasks: GC-content bias correction (using HMMcopy) a. Computing read coverage from ULP-WGS b. Data correction and normalization CNA prediction and estimation of tumor fraction of cfDNA

workflow for estimating the fraction of tumour in cell-free DNA from sWGS - oicr-gsi/ichorCNA

Default: [%default]"), make_option (c ("--minTumFracToCorrect"), type="numeric", default=0.1, help = "Tumor-fraction correction of bin and segment-level CNA if sample has minimum …

ichorCNA_U is a modified version of ichorCNA v0.3.2 that removes hard-coded human-specific chromosome name requirments, enabling ichorCNA to be run on a wider range of species. It also adds a slurm-compatible wrapper for high-throughput analysis of many samples, and generation of a summary table with tumor fractions and stats from the highest likelihood solutions. The original ichorCNA source ...

The analysis workflow consists of 2 tasks: GC-content bias correction (using HMMcopy) a. Computing read coverage from ULP-WGS b. Data correction and normalization CNA …

Nov 20, 2019 · Hi @CuriusScientist and @lbeltrame Thank you for bringing up this issue. I had introduced a problem with the plotting in a recent commit. It only affects low tumor fraction samples. Briefly, the copy number correction step was being applied to low tumor fraction samples. I can provide a quick fix here to make sure not to do that for cases/solutions having < 0.05 TF. Sorry for the inconvenience ...

Estimating tumor fraction by exploiting the off-target reads from targeted DNA sequencing. - GavinHaLab/ichorCNA_offtarget

Aug 29, 2018 · Hi, I have pasted code below of error when running ichor_CNA snakemake: Error in optim (n_prev, fn = completeLikelihoodFun, pType = rep ("n", S), : 2 L-BFGS-B needs finite values of 'fn' 1 Calls: HMMsegment -> runEM -> estimateParamsMap Do...