Options Specific to Mapping

4.3	Options Specific to Mapping

Option	Description	runMapping	runProject (Mapping)	gsMapper
-gref	Flag for genomic reference sequence	X (also for setRef)	X	Reference type selection
-cref	Flag for cDNA reference sequence	X (also for setRef)	X	Reference type selection
-accno filename	Flag to specify an accno renaming file, to allow reference accession numbers and descriptions to be changed in the generation of the output.	X	X	Parameter: Accno renaming file
-noaccno	Flag to deactivate use of an accno renaming file	X	X
-random	Flag to allow GOLDENPATH _random and _hap references to be automatically used.	X
-ref/-read	Flags to separate reference & read files	X
‑n, ‑nimblegen	Flag to specify reads should be primer-trimmed using the early NimbleGen Sequence Capture protocol’s primer sequence	X	X	Parameters: Nimblegen Sequence Capture toggle
-non, nonimblegen	Flag to turn off NimbleGen mapping mode	X	X	Parameters: Nimblegen Sequence Capture toggle
-annot filedesc	Flag for optional file with gene-coding/region annotation for reference sequence(s) for gene name and protein translation info in Variant GUI tab	X	X	Parameters: Genome Annotation
-noannot	Flag to disable the automatic reading of annotation file	X	X	Parameters: Genome Annotation (leave blank)
-snp filedesc	Flag for optional file with known SNP information for the reference sequence(s) for linking to identified variations on the HCDiffs GUI tab	X	X	Parameters: Known SNP
-nosnp	Flag to disable the automatic reading of known SNP files	X	X	Parameters: Known SNP (leave blank)
-rst	Flag to set the repeat score threshold parameter	X	X	Parameters: Repeat score threshold
-hll	Flag to set the Hit location limit parameter (no longer used in v2.3 algorithm, default set to 1,000,000)	X	X	Parameters: Hit location limit
-hsl	Flag to set the Hit-per-seed limit parameter (new default value of 70, optimized for newer algorithms)	X	X	Parameters: Hit per seed limit
-d	Flag to set the minimum contig depth	X	X	Parameters: Minimum contig depth
-fd	Flag to specify full variant file details	X	X	Parameters: Full variant file details
-nobam	Flag to suppress bam file generation	X	X	Parameters: BAM Output: No files Selected
-bam	Flag to generate bam file containing the multiple alignments for the contigs.	X	X	Parameters: BAM Output: Single file Selected
-srv	Flag to enable single read variant output	X	X	Parameters: Single read variant Toggle
-nor	Flag to disable single read variant output	X	X	Parameters: Single read variant Toggle
-reg accno:# - # or regstringfile or Nimblegen DARFile	Flag to only output specified sequence region of the reference and aligned reads	X	X	Parameters: Config files; Targeted Regions
-noreg	Flag to turn off sequence region based generation of output		X	Parameters: Config files; Targeted Regions (leave blank)

Table 6: Options Specific to Mapping