1. Snakemake Pipeline

See instructions for snakemake pipeline

2. ichorCNA R script details

The main ichorCNA R script can also be run with even more exposed options once WIG files for read counts have been generated.

Here is an example of how to launch the R script from the command line:

Rscript ../runIchorCNA.R --libdir ../../R/ --datadir ../../inst/extdata/ \
  --id tumor_sample1 --WIG results/readDepth/tumor_sample1.bin1000000.wig \
  --ploidy "c(2,3)" --normal "c(0.5,0.6,0.7,0.8,0.9)" --maxCN 5 \
  --includeHOMD False --chrs "c(1:22, \"X\")" --chrTrain "c(1:22)" \
  --estimateNormal True --estimatePloidy True --estimateScPrevalence True \
  --scStates "c(1,3)" --centromere ../../inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt \
  --exons.bed None --txnE 0.9999 --txnStrength 10000 --plotFileType png --plotYLim "c(-2,4)" \
  --outDir results/ichorCNA/tumor_sample1/ > logs/ichorCNA/tumor_sample1.log 2> logs/ichorCNA/tumor_sample1.log

The list of arguments that can be passed to the script by invoking --help:

>Rscript runIchorCNA.R --help

Usage: runIchorCNA.R [options]

        -l LIBDIR, --libdir=LIBDIR
                Script library path

                Reference wig dir path

        -t WIG, --WIG=WIG
                Path to tumor WIG file.

                Path to normal WIG file.

                Median corrected depth from panel of normals

        -e EXONS.BED, --exons.bed=EXONS.BED
                Path to bed file containing exon regions.

                Patient ID.

        -n NORMAL, --normal=NORMAL
                Initial normal contamination

                Subclonal states to consider

        -p PLOIDY, --ploidy=PLOIDY
                Initial tumour ploidy

        -m MAXCN, --maxCN=MAXCN
                Total clonal CN states

                Estimate normal.

                Estimate subclonal prevalence.

                Estimate tumour ploidy.

 (plus more arguments)

broadinstitute/ichorCNA documentation built on Dec. 25, 2019, 3:12 a.m.