Sets parameters for the SNP computation phase of the assembly. The command is designed for use with existing BAM files that have not been analyzed for SNPs, or to re-analyze an existing file with different parameters.
Most of the parameters for computeSNP are identical to parameters for assembleTemplate and are discussed in that topic:
showCDSVariant
snp_logLevel
snp_minProbNonrefToCall
snp_checkStrandedness
snp_logStartPos
snp_minStrandCov
snp_combineSubs
snp_logTemplateID
snp_minVariantDepthToScore
snp_excludeBases3p
snp_maxRun
snp_minWeight
All other parameters are described in the table below:
| Parameter | Description | Allowed values (defaults are underlined) |
|---|---|---|
| calcJunctionSeqs | In the structural variation workflow, specifying ‘false’ prevents junction sequences from being calculated. | [ true / false ] |
| concurrentAligns | (Intended for internal use only) | [number] |
| file | (required) Specifies the path and name of one or more .assembly projects from which to compute SNPs. | [directory/filename enclosed in quotes] |
| snp_writeMissingDBSnps | In a SNP assembly, specifying ‘false’ causes missing SNPs not to be recorded, saving time and file space. | [ true / false ] |
| snpFilter | Specifies whether SNP filtering is turned on or off. Properties for snpFilter: capture: [ true / false ] Specifies whether there is an exome capture file. If an exon capture file is added in the SeqMan NGen wizard or through a script, this value is set to ‘true.’ In the absence of an exome capture file, the SeqMan NGen wizard automatically sets this property to ‘false.’ pNotRefMinVal: [number] In the unusual case that the hard filter is missing, this property is used to set the minimum value that can be displayed in the SeqMan SNP table. Otherwise, this property is ignored. Default is 10. userOnly: [ true / false / All ] Specifies whether there is a VCF SNP file. The SeqMan NGen wizard always calls this as ‘true’ (or ‘yes’) but ignores the property if no VCF SNP file has been loaded. pNotRef: [number] This parameter is equivalent to Wizard option Assembly Options > SNP Filter Stringency > pNotRef. This parameters is a “soft” filter used to specify a PnotRef threshold. Data not matching the criterion are removed from the default display of the SeqMan Pro SNP table. This option is only available for the Bayesian SNP calling methods (used when genome ploidy is “Diploid” or “Haploid”). Wizard values include Low (90%), Medium (99%) and High (99.9%). minSnpFilter: [number] This parameter does not relate to any setting in the SeqMan NGen wizard, but corresponds to “SNP%” in SeqMan Pro and “minSNPFilter” in ArrayStar. In the simple SNP calling method (used when genome ploidy is “Heterogeneous”), the default is 5% for 454 and Ion Torrent read technologies; 1% for all others. In Bayesian SNP calling methods (used when genome ploidy is “Diploid” or “Haploid”), the default depends on stringency and ploidy rather than the read technology. The default for Diploid is 15% for all stringency levels. The default for Haploid is 25% for low stringency, 50% for medium and 75% for high. minDepth: [number] (optional) Specifies a minimum sequence depth threshold. This parameter does not relate to any setting in the SeqMan NGen wizard, but corresponds to Depth in SeqMan Pro and minDepth in ArrayStar. In the simple SNP calling method (used when genome ploidy is “Heterogeneous”), the default is 50. In Bayesian SNP calling methods (used when genome ploidy is Diploid or Haploid), the default is 20. The following set of SNP filters are used by ArrayStar and SeqMan Pro: codonOnly: [ Coding / CodingChange / Nonsense / All ] maxDepth: [number] maxCodingFeatureDistance: [number] minSnpFilter: [number] qCall: [number] synonymousCodingChange: [true/false] substitionCodingChange: [true/false] noStartCodingChange: [true/false] noStopCodingChange: [true/false] nonsenseCodingChange: [true/false] frameshiftCodingChange: [true/false] notCodingCodingChange: [true/false] inFrameIndelCodingChange: [true/false] refOnly: [Reference/Unique/All] cosmicOnly : [Yes/No/All] minIndelSize: [number] gerpScore: [number] substitution: [true/false] showIndels: [true/false] |
|
| userSNP | Specifies a location for storing the VCF SNP table. | [directory/filename enclosed in quotes] |
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