The command loadBAM is used to set parameters for analyzing existing BAM files. It allows ungapped BAM files to be converted into a fully gapped assembly file or to re-gap an existing file with different parameters. The command also permits SNPs to be calculated or re-calculated with different parameters starting with an existing BAM file. The associated parameters are also available for full assemblies and are described under the assembleTemplate command.
| Parameter | Allowed values |
|---|---|
| align | |
| delayAlignInserts | [true|false] |
| format | |
| gapPenalty | |
| increaseRunGapPen | [true|false] |
| layout | |
| matchScore | |
| minAlignedLength | [0-999] |
| minMatchPercent | |
| mismatchPenalty | |
| output | |
| removeUniqueInserts | [true|false] |
| snp | |
| snp_checkStrandedness | |
| snp_clusteredPosFilterMinDev | [number] |
| snp_clusteredPosFilterMinFromEdge | [number] |
| snp_hetKnownThresh | [number] |
| snp_hetThresh | [number] |
| snp_limitEndPos | |
| snp_limitStartPos | |
| snp_limitTemplateID | |
| snp_logEndPos | |
| snp_logLevel | |
| snp_logStartPos | |
| snp_logTemplateID | |
| snp_maxRun | [number] |
| snp_maxStrandBias | [number] |
| snp_minHomopolDelDepth | [number] |
| snp_minHomopolDelFrac | [number] |
| snp_minHomopolInsDepth | [number] |
| snp_minHomopolInsFrac | [number] |
| snp_minPctToScore | |
| snp_minProbNonrefToCall | |
| snp_minStrandCov | [number] |
| snp_minVariantDepthToScore | |
| snp_minWeight | |
| snp_nlMutationRate | The chance that any single base is different from the reference. The default value of 0.0013 is equivalent to ~4 million variations in a Human sample against the reference or several thousand in a bacterial genome. [number] |
| snp_observedInControlFilterMaxCount | [number] |
| snp_observedInControlFilterMaxFrac | [number] |
| snp_proximalGapFilterMaxDel | [number] |
| snp_proximalGapFilterMaxIns | [number] |
| snp_proximalGapFilterWindowSize | [number] |
| snp_reportUserMissing | [dbSNP|user|zeroCoverage|cosmic|allcaptured|captured] |
| snp_runVar | [true|false] |
| snp_showAllFeatures | [true|false] |
| snp_writeExtended | |
| snp_writeMissingDBSnps | [true|false] |
| snpMethod | |
| snpRefAsm | [quoted file name] |
| template |
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