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
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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