This Seqware workflow is a wrapper for HMMcopy which is a CNV analysis tool capable of making calls using paired Normal/Tumor data. The tool detects copy-number changes and allelic imbalances (including LOH) using deep-sequencing data.Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.
java -jar cromwell.jar run hmmcopy.wdl --inputs inputs.json
| Parameter | Value | Description |
|---|---|---|
inputTumor |
File | input .bam file for tumor sample |
inputNormal |
File | input .bam file for normal sample |
reference |
String | reference assembly id |
| Parameter | Value | Default | Description |
|---|---|---|---|
outputFileNamePrefix |
String | "" | Output file(s) prefix |
| Parameter | Value | Default | Description |
|---|---|---|---|
normalConvert.modules |
String | "hmmcopy-utils/0.1.1" | required modules, basicall hmmcopy utils |
normalConvert.readCounter |
String | "$HMMCOPY_UTILS_ROOT/bin/readCounter" | Path to readCounter utility |
normalConvert.chromosomes |
String? | None | comma-separated list of chromosomes to use, default is ALL |
normalConvert.window |
Int? | None | Resolution of a bin, in bases, default is 1000 |
normalConvert.jobMemory |
Int | 8 | memory for this job, in Gb |
normalConvert.timeout |
Int | 20 | Timeout in hours, needed to override imposed limits |
tumorConvert.modules |
String | "hmmcopy-utils/0.1.1" | required modules, basicall hmmcopy utils |
tumorConvert.readCounter |
String | "$HMMCOPY_UTILS_ROOT/bin/readCounter" | Path to readCounter utility |
tumorConvert.chromosomes |
String? | None | comma-separated list of chromosomes to use, default is ALL |
tumorConvert.window |
Int? | None | Resolution of a bin, in bases, default is 1000 |
tumorConvert.jobMemory |
Int | 8 | memory for this job, in Gb |
tumorConvert.timeout |
Int | 20 | Timeout in hours, needed to override imposed limits |
runHMMcopy.rScript |
String | "$RSTATS_ROOT/bin/Rscript" | Path to Rscript |
runHMMcopy.hmmcopyScript |
String | "$HMMCOPY_SCRIPTS_ROOT/run_HMMcopy.r" | Path to .R script that runs HMMcopy pipeline |
runHMMcopy.jobMemory |
Int | 8 | memory in GB for this job |
runHMMcopy.timeout |
Int | 20 | Timeout in hours, needed to override imposed limits |
| Output | Type | Description |
|---|---|---|
resultiSegFile |
File | .seg file produced with HMMcopy |
resultTsvFile |
File | .tsv file with all calls produced by HMMcopy |
cgBiasImage |
File | Plot showing the results of CG bias test |
segImage |
File | Plot shows the segmentation data |
This section lists command(s) run by hmmcopy workflow
- Running hmmcopy
HMMcopy workflow uses R package hmmcopy utilizing custom R scripts.
Pre-processing:
READ_COUNTER -b INPUT_FILE
READ_COUNTER -w WINDOW (Optional) -c CHROMOSOMES (Optional) INPUT_FILE > INPUT_FILE_BASENAME_reads.wig
Running the analysis:
Rscript HMMCOPY_SCRIPT NORMAL_WIG TUMOR_WIG CG_FILE MAP_FILE OUTPUT_PREFIX
zip -q OUTPUT_PREFIX_images.zip *.png
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
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