FREEC 2.0
java -jar cromwell.jar run freec.wdl --inputs inputs.json
| Parameter | Value | Description |
|---|---|---|
inputTumor |
File | Input .bam file for analysis sample |
sequencingType |
String | One of WG, EX or TS |
reference |
String | Reference assembly id |
| Parameter | Value | Default | Description |
|---|---|---|---|
inputNormal |
File? | None | Optional input .bam file for control sample |
bedgraphOutput |
Boolean | true | String that says TRUE or FALSE, determines if we need BedGraph output or not |
outputFileNamePrefix |
String | "" | Prefix for outputs |
| Parameter | Value | Default | Description |
|---|---|---|---|
runFreec.intervalFile |
String? | None | Optional path to an interval .bed file, for targeted sequencing like EX, TS |
runFreec.coefficientOfVariation |
Float | 0.05 | Parameter for CNV calling, default is 0.05 |
runFreec.breakPointThreshold |
Float | 0.8 | Parameter for CNV calling, default is 0.8 |
runFreec.contaminationAdjustment |
String? | None | informs FREEC about expected degree of contamination with normal tissue |
runFreec.contaminationFraction |
Float | 0.0 | Contaminating fraction, by default is 0 |
runFreec.window |
Int | 1000 | Defines the resolution of the analysis, default:1000 |
runFreec.jobMemory |
Int | 20 | Memory in Gb for this job |
runFreec.maxThreads |
Int | 4 | Maximum threads for the process, default is 4 |
runFreec.telocentromeric |
Int | 50000 | For human, we need 50000 (default) |
runFreec.inputFormat |
String | "BAM" | Maybe SAM, BAM, pileup, bowtie, eland, arachne, psl (BLAT), BED. We use BAM |
runFreec.mateOrientation |
String | "FR" | For paired-end Illumina we need FR, other types are also supported |
runFreec.configFile |
String | "config_freec.conf" | config_freec.conf |
runFreec.logPath |
String | "freec_run.log" | We have a log file which is not provisioned but can be examined if anything goes wrong |
runFreec.timeout |
Int | 72 | Timeout in hours, needed to override imposed limits |
| Output | Type | Description | Labels |
|---|---|---|---|
infoFile |
File | Info file for the calls | vidarr_label: infoFile |
regionFile |
File | Region File | vidarr_label: regionFile |
ratioFile |
File | Ratio File | vidarr_label: ratioFile |
cnvTumor |
File | CNV for tumor file | vidarr_label: cnvTumor |
cnvNormal |
File? | CNV for normal file | vidarr_label: cnvNormal |
gcProfile |
File? | GC profile data | vidarr_label: gcProfile |
ratioBedGraph |
File? | Retio BedGraph data | vidarr_label: ratioBedGraph |
This section lists command(s) run by freec workflow
- Running freec
FREEC is a CNV-calling tool which may run in a control-free (Tumor-only) mode. This workflow runs a custom python script which assembles a config file using the provided inputs
Writing a config file given the inputs
...
freec --conf iCONFIG_FILE >> LOG_PATH
...
Post-processing and renaming of files
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
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