msisensor
Microsatelite Instability (MSI) detection using msisensor-pro
Overview
Dependencies
Usage
Cromwell
java -jar cromwell.jar run msisensor.wdl --inputs inputs.json
Inputs
Required workflow parameters:
| Parameter | Value | Description |
|---|---|---|
normalbam |
File | normal input .bam file |
normalbai |
File | normal input .bai file |
tumorbam |
File | tumor input .bam file |
tumorbai |
File | tumor input .bai file |
boostrapIt |
Boolean | Enable bootstrapping |
reference |
String | reference genome of input sample |
Optional workflow parameters:
| Parameter | Value | Default | Description |
|---|---|---|---|
outputFileNamePrefix |
String | basename("~{tumorbam}",".bam") | Base name |
Optional task parameters:
| Parameter | Value | Default | Description |
|---|---|---|---|
runMSIsensor.outputFileNamePrefix |
String | basename("~{tumorbam}",".bam") | Base name |
runMSIsensor.difficultRegions |
String? | None | Path to .bed of difficult regions to exclude |
runMSIsensor.jobMemory |
Int | 64 | Memory allocated for this job (GB) |
runMSIsensor.threads |
Int | 4 | Requested CPU threads |
runMSIsensor.timeout |
Int | 10 | Hours before task timeout |
bootstrapMSIsensor.boots |
Int | 100 | number of bootstraps |
bootstrapMSIsensor.loci |
Int | 500 | number of loci to include in each bootstrap |
bootstrapMSIsensor.outputFileNamePrefix |
String | basename("~{tumorbam}",".bam") | Base name |
bootstrapMSIsensor.jobMemory |
Int | 64 | Memory allocated for this job (GB) |
bootstrapMSIsensor.threads |
Int | 4 | Requested CPU threads |
bootstrapMSIsensor.timeout |
Int | 10 | Hours before task timeout |
bootstrapMSIsensor.difficultRegions |
String? | None | bed file of regions to avoid, if necessary |
Outputs
| Output | Type | Description |
|---|---|---|
msiGermline |
File | A poorly documented output, ostensibly germline-specific metrics for MSI sites |
msiSomatic |
File | A poorly documented output, ostensibly somatic-specific metrics for MSI sites |
msiFinalOutput |
File | Final msisensor call as .tsv, last column is msi score |
msibooted |
File? | msisensor calls bootstrapped |
Commands
This section lists command(s) run by msisensor workflow
- Running msisensor
Microsatelite Instability (MSI) detection using msisensor-pro. MSIsensor-pro is an updated version of msisensor. MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with NGS data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative sites selection method to enable MSI detection without matched normal samples.
Run msisensor-pro (the main step)
set -euo pipefail
msisensor-pro msi
-d MSIFILE
-e difficultRegions (Optional)
-n NORMAL_BAM
-t TUMOR_BAM
-o BASENAME.msi
Optional bootstrapping with the same inputs:
set -euo pipefail
for boot in {1..~{boots}}
do
shuf -n ~{loci} ~{msifile} > rep.list
sort -k1,1 -k2,2n rep.list > rep.list.sorted
msisensor-pro msi
-d rep.list.sorted
-e difficultRegions (Optional)
-n NORMAL_BAM
-t TUMOR_BAM
-o BASENAME.msi
awk -v boot="${boot}" '$1 !~ "Total_Number_of_Sites" {print boot"\t"$1"\t"$2"\t"$3}' ~{basename}.msi >> ~{basename}.msi.booted
done
Support
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)