View source: R/run.vardict.sample.R
Run VarDict on a sample. Idea: have a low-level function that simply submits job to Perl, after BAM paths have been found. and output paths already have been decided upon
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tumour.bam |
Path to tumour sample BAM file. |
sample.id |
Sample ID for labelling |
paired |
Logical indicating whether to do variant calling with a matched normal. |
proton |
Logical indicating whether the data was generated by proton sequencing. Defaults to False (i.e. Illumina) |
normal.bam |
Path to normal BAM file if |
output.directory |
Path to output directory |
output.filename |
Name of resulting VCF file (defaults to SAMPLE_ID.vcf) |
code.directory |
Path to directory where code should be stored |
log.directory |
Path to directory where log files should be stored |
config.file |
Path to config file |
job.dependencies |
Vector with names of job dependencies |
job.name |
Name of job to be submitted |
job.group |
Group job should belong to |
quiet |
Logical indicating whether to print command to screen rather than submit it to the system. Defaults to false, useful for debugging. |
verify.options |
Logical indicating whether to run verify.varitas.options |
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