Pisces 5.1.3 Arguments

Example command line call:

Pisces.exe -BamPaths \path\to\my_S1.bam,\path\to\my_S2.bam -g D:\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA -f 0.01 -fo True -b 20 -q 100 -c 10 -gVCF True -i \path\to\my_interval_file1.txt,\path\to\my_interval_file2.txt -CallMNVs true -MaxMNVLength 3 -MaxGapBetweenMNV 1

Key To Icons In The Table Below:

Safety Category

• ✅ Required input parameter
• ❇️ Optional input parameter
• ⚠️ Experimental or dev use only.

Parameter Category

• 😷 Causes variants to be marked as filtered in the (g)VCF.
• 🚫 Causes variants to be omitted from the (g)VCF.
• 🔧 The value is an internal algorithm parameter
• 🛄 Sets input / output files or destinations

Pisces Argument Table:

Argument	Type	Default	Description	Safe?	Category
-a, -MinVariantQScore	Integer	20	Minimum variant quality score needed to emit variant.	❇️	🚫omits variant
-B, -BamPaths	String	None	File path(s) for input bam(s). This can be a single value or comma-separated list of multiple file paths.	✅	🛄input
-b, -MinBaseCallQuality	Integer	20	Minimum basecall quality for a base to contribute to variant calling. Note that as well as filtering base calls, this also drives Pisces internal noise model. (ie, if all bases are Q20 and above, Pisces has believes that the noise rate is 1/100, and uses that to drive decisions) Must be between 0 and 50.	✅	🔧parameter
-BAMFolder	String	None	Parent BAM Folder. Must be provided if –B, i.e BAMPath(s). is not specified.	✅	🛄input
-c, -MinCoverage	Integer	10	Minimum coverage allowed. (variant will be omitted or converted to a nocall if in gVCF mode)	❇️	🚫omits variant
-CallMNVs, -PhaseSNPs	Boolean	FALSE	Whether or not to call MNVs.	❇️	🔧parameter
-ChrFilter	String	None	Debug option to variant call just the specified chromosome	❇️	🔧parameter
-Collapse	Boolean	FALSE	Whether or not to collapse variants together, 'true' or 'false'.	⚠️	🔧parameter
-CoverageMethod	String	approximate	'approximate' or 'exact' .	⚠️	🔧parameter
-CrushVcf, -crushvcf	Boolean	FALSE	Normally gVcfs are output in the "somatic" format, which has one line per allele. A crushed vcf is more standard in the germline world, with one line per genomic loci. Note: typically set to true in conjunction with the '-Ploidy diploid' option.	❇️	🔧parameter
-DiploidGenotypeParameters	Float,Float,Float	0.20,0.70,0.80	Comma-separated list of three numbers A,B,C between 0 and 1.A = minimum allele frequency to be detected as 0/1. B = maximum allele frequency to be detected as 0/1. C= minimum value for the sum of alleles 1 and 2. Ie, if C is not met, the site is flagged as 'Multiallelic'	⚠️	🔧parameter
-f, -minimumfrequency, -MinimumFrequency	Float	0.01	Minimum variant frequency allowed. Only affects somatic calling. Diploid calling uses a different parameter. Must be between 0 and 1.	❇️	🚫omits variant
-F, -variantqualityfilter, -VariantQualityFilter	Integer	30	Threshold for variant quality score filter. FilteredVariantQScore to report variant as filtered	❇️	😷filter
-v, -MinVariantFrequencyFilter,	Float	None	FilteredVariantFrequency to report variant as filtered	❇️	😷filter
-fo, -EnableSingleStrandFilter	Boolean	FALSE	Flag variants as filtered if coverage limited to one strand. If all available reads go in one direction, this will filter everything.	✅	😷filter
-g, -GenomePaths	String	None	Directory path for genome. This can be a single value or a comma-separated list of multiple genome paths.The genome used must match the genome used to create the input bam file. If multiple paths provided, the number of paths must match the number of bam paths provided in –B. Must be single value if -BAMFolder is specified	✅	🔧parameter
-gt, -GT, -GTModel	String	‘threshold’	Genotype model. Models other than thresholding are currently not available.	⚠️	🔧parameter
-gtq, -genotypequalityfilter, -GenotypeQualityFilter	Integer	None	Filters variants if genotype quality is below the given threshold. Should be greater than 0.	❇️	😷filter
-gVCF	Boolean	FALSE	Whether or not to produce genome vcfs, which include reference calls.	❇️	🔧parameter
-i, -IntervalPaths	String	None	File path for interval file. This can be a single value or comma-separated list of interval paths. If provided, file path(s) must exist. If multiple paths provided, the number of paths must match the number of bam paths provided in –B. Must be single value if -BAMFolder is specified	❇️	🛄input
-ld, -MinDepthFilter	Integer	None	Filters variants if the total coverage depth is below the given threshold. Should be above the minimum coverage depth to emit a variant.	❇️	😷filter
-m, -MinMapQuality	Integer	1	Minimum alignment quality score, a.k.a. map score. Must be 0 or greater.	❇️	🔧parameter
-MaxFragmentSize	Integer	1000	When stitching is enabled, this is the max fragment size allowed when pairing. Reads without a mate found within this window are skipped.	⚠️	🔧parameter
-MaxGapBetweenMNV, -MaxGapPhasedSNP, -MaxRefGapInMnv	Integer	1	Maximum length of reference span contained in MNV. Must be 0 or greater.	❇️	🔧parameter
-MaxGenotypeQScore	Integer	100	Upper bound for genotype Q score. Must be 0 or greater.	❇️	🔧parameter
-MaxMNVLength, -MaxPhasedSNPLength, -MaxPhaseSNPLength	Integer	3	Maximum length for MNVs. Must be between 1 and 1000.	❇️	🔧parameter
-MinGenotypeQScore	Integer	0	Lower bound for genotype Q score calculation. Must be 0 or greater.	❇️	🔧parameter
-Mono	String	None	Explicit path to mono. When -ThreadingByChr on the linux cluster, mono might not be detectable on every node as an environment variable, or the preset mono might not be the same version called by the user at the command line. If you are plagued by mono issues, use this to explicitly set the mono path.	⚠️	🔧parameter
-NifyDisagreements	Boolean	FALSE	When stitching is enabled, change any disagreeing bases in the overlap region to 'N'. (By default, when bases disagree, the base with the best base call Q score is taken)	⚠️	🔧parameter
-NL, -NoiseLevelForQModel	Integer	Same value as minimum basecall quality	By default, the noise level is taken to be the minimum basecall quality used, but it can be overridden here. The noise level is then fed into the variant Q score algorithms to determine the change of a false positive. Must be 0 or greater	⚠️	🔧parameter
-o, -OutputSBFiles	Boolean	FALSE	Whether or not to output strand bias calculation files.	❇️	🔧parameter
-OutFolder	String	FALSE	Directory path in which to generate output and log files.	❇️	🛄output
-p, -OnlyUseProperPairs	Boolean	FALSE	Whether or not to only use alignments that are properly paired.	❇️	🔧parameter
-ploidy, -Ploidy	String	'somatic'	Available ploidy models are 'somatic' or 'diploid' . The ploidy model one input to determining the genotype of a variant. Note: '-CrushVcf true' should be used with this option to get the germline-standard formatted vcf, where co-located alleles show up on the same vcf line.	❇️	🔧parameter
-PriorsPath	String	None	Path to vcf file containing known variants, used with -collapse to preferentially reconcile variants	⚠️	🔧parameter
-q, -MaxVariantQScore	Integer	100	Upper bound for variant qscore calculation. Must be greater than 0. Must be greater than or equal to MinimumVariantQscore.	❇️	🔧parameter
-repeatfilter, -RepeatFilter	Integer	None, off	Filters out indels, when the insertion or deletion is an exact match for the repeat element in a region of N repeats of the element. See the SDS for details. Should between 0 and 10	❇️	😷filter
-ReportNoCalls	Boolean	FALSE	Whether or not to report fraction no calls in the vcf.	❇️	🔧parameter
-ReportRcCounts	Boolean	FALSE	Debug option. When BAM files contain X1 and X2 tags, output read counts for duplex-stitched, duplex-nonstitched, simplex-stitched, and simplex-nonstitched.	⚠️	🔧parameter
-RMxNFilter	Integer,Integer (or set to FALSE to turn off)	5,9	Filters out indels, when the insertion or deletion is bookended by an exact match (of length <=M) for the repeat element in a region of >= N repeats of the element. SDS for details. Value must be bool or M,N format	⚠️	😷filter
-s, -MaxAcceptableStrandBiasFilter	Float	0.5	Threshold for strand bias filter. Must be greater than 0.	❇️	😷filter
-SBModel	String	Extended	Strand bias model. Must be ‘poisson’ or ‘extended’.	❇️	🔧parameter
-StitchPairedReads	Boolean	FALSE	Whether or not to stitch overlapping reads pairs. If you use this, also turn on UseXCStitcher	⚠️	🔧parameter
-t,-MaxNumThreads	Integer	10	Maximum number of threads. Must be 1 or greater.	❇️	🔧parameter
-ThreadByChr	Boolean	FALSE	Whether or not to parallel process by chromosome. Might require the -Mono argument on some cluster configurations.	⚠️	🔧parameter
-TrimMnvPriors	Boolean	FALSE	Whether or not to trim preceeding base from MNVs in priors file. COSMIC convention is to include preceeding base for MNV, which is NOT the pisces convention. So, if you are using -collapse true and -priorsFile /mypriorsfile.vcf and your file defies Pisces MNV convention you need this.	⚠️	🔧parameter
-UnstitchableStrategy	String	'both'.	When stitching is enabled, the strategy for handling unstitchable reads, 'both' (process both reads separately), 'stronger' (take the read with higher quality), or 'none' (throw out the unstitchable pair). Must be 'both' , 'stronger', or 'none'	⚠️	🔧parameter
-XcStitcher	Boolean	TRUE	UseXCStitcher 'true' or 'false'. Stitching reads without XCStitcher is still experimental at best. This should be ON anytime -StitchPairedReads is on.	⚠️	🔧parameter