GotCloud: Variant Calling Options
From Genome Analysis Wiki
| Command-line Flag | Configuration Key | Value Description | Default Value |
|---|---|---|---|
| --help | print help information | ||
| --test path | run the snpcall/ldrefine test and write output to the specified path | ||
| --conf file | configuration file to use | ||
| --numjobs # | number of jobs to run in parallel | 0 (generate Makefile of steps, but do not run) | |
| --maxlocaljobs # | maximum # of jobs that can run if batchtype is local (to prevent accidentally starting jobs locally that were meant to be on a cluster) | 10 | |
| --outdir path | OUT_DIR | output directory | |
| --list/--bam_list/--bamlist file | BAM_LIST | path to the BAM List File | $(OUT_DIR)/bam.list |
| --chrs # # | CHRS | pace separated list of chromosomes to process | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X |
| --region #:#-# | call region - skip regions of chromosome outside of specified region
format (-end is optional): chr:start-end |
||
| --makebasename name | MAKE_BASE_NAME | basename of the Makefile generated by GotCloud | umake |
| --batchtype type | BATCH_TYPE | name of cluster type | local |
| --batchopts opts | BATCH_OPTS | options to pass to the cluster command | |
| --bamprefix prefix | BAM_PREFIX | path to prepend to relative BAM file paths in the BAM list | |
| --refprefix prefix | REF_PREFIX | path to prepend to relative reference/resource file paths | |
| --baseprefix prefix | BASE_PREFIX | path to prepend to relative paths for the BAM list file, PED_INDEX, BAM (if BAM_PREFIX isn't specified), reference/resource files (if REF_PREFIX isn't specified) | |
| --refdir path | REF_DIR | value to use for REF_DIR key | $(GOTCLOUD_ROOT)/gotcloud.ref |
| --verbose | Add additional messages when reading configuration | ||
| --copyglf path | COPY_GLF | path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp) | |
| --ignoresmcheck | IGNORE_SM_CHECK | disable the validation that the Sample name in the BAM file matches the one in the BAM list file | |
| --gotcloudroot path | GOTCLOUD_ROOT | specify to use a different directory for finding GotCloud bins/scripts | based on the location of the gotcloud/umake.pl script |
| --nophonehome | disable phonehome in GotCloud and the tools it calls |
