Pisces 5.2.10 Supported Options

Example command line call:

dotnet Pisces.dll -bam \path\to\my_S1.bam,\path\to\my_S2.bam -g \Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA

Notes:

Arguments are now capitalization invariant.

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
MinVariantQScore	Integer	20	Minimum variant quality score needed to emit variant.	❇️	🚫omits variant
bam	String	None	File path(s) for input bam(s). This can be a single value or comma-separated list of multiple file paths. If a single directory is input, all bams in the directory will be processed.	✅	🛄input
MinBaseCallQuality, MinBQ	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
c, MinDepth, MinDP	Integer	10	Minimum coverage allowed. (variant will be omitted or converted to a nocall if in gVCF mode)	❇️	🚫omits variant
CallMNVs	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	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
Debug	Boolean	FALSE	Whether or not to run in debug mode. Debug mode produces extra files/logs.	⚠️	🔧parameter
ForcedAlleles	String	Null	(vcf file path) Input a vcf file to force pisces to output specific supplied variants. Must turn off crushvcf.	⚠️	🛄input
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
MinimumFrequency,MinVF	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
VQFilter,VariantQualityFilter	Integer	30	Threshold for variant quality score filter, to report variant as filtered	❇️	😷filter
VFFilter, MinVariantFrequencyFilter	Float	None	FilteredVariantFrequency to report variant as filtered	❇️	😷filter
SSFilter, 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
GQFilter, 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
Gender	Boolean	FALSE	Whether or not sample is known to be male. Used in ploidy calculation. Default, no gender assumption. Male=TRUE, Female=FALSE. Only affects germline-mode results.	❇️	🔧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
MinDPFilter, 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
MinMQ,MinMapQuality	Integer	1	Minimum alignment quality score, a.k.a. map score. Must be 0 or greater.	❇️	🔧parameter
MaxGapBetweenMNV, MaxRefGapInMnv	Integer	1	Maximum length of reference span contained in MNV. Must be 0 or greater.	❇️	🔧parameter
MaxGQ,MaxGenotypeQScore	Integer	100	Upper bound for genotype Q score. Must be 0 or greater.	❇️	🔧parameter
MaxMNVLength	Integer	3	Maximum length for MNVs. Must be between 1 and 1000.	❇️	🔧parameter
MinGQ, MinGenotypeQScore	Integer	0	Lower bound for genotype Q score calculation. Must be 0 or greater.	❇️	🔧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
NoiseModel	String	Flat	'window' or 'flat'. If 'flat' is selected, the same noise level will be assumed for all loci when calculating the variant call Q score. By default, this is q20. If 'window' is selected, the average noise level in a window around the variant will be calculated based on local base call Q scores. (The window size is currently hard coded to 1). In practice, we have found keeping the applied noise level coupled to the minimum basecall quality to be the most effective.	❇️	🔧parameter
OutputSBFiles	Boolean	FALSE	Whether or not to output strand bias calculation files.	❇️	🔧parameter
Out,OutFolder	String	FALSE	Directory path in which to generate output and log files.	❇️	🛄output
pp,OnlyUseProperPairs	Boolean	FALSE	Whether or not to only use alignments that are properly paired.	❇️	🔧parameter
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
MaxVQ,MaxVariantQScore	Integer	100	Upper bound for variant qscore calculation. Must be greater than 0. Must be greater than or equal to MinimumVariantQscore.	❇️	🔧parameter
FilterDuplicates,DuplicateReadFilter	Bool	True	Filter out reads marked as duplicates. Reads should already be marked as duplicates by an upstream application.	❇️	😷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,Float (or set to FALSE to turn off)	5,9,0.20	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,F format. Default, kicks in for 20% VF and below. Raise to 35% if needed.	⚠️	😷filter
SBFilter, 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
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.	⚠️	🔧parameter
TrimMnvPriors	Boolean	FALSE	Whether or not to trim preceding 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
UseStitchedXD	Boolean	FALSE	Whether or not expect an XD (stitched direction tag) from a Gemini bam. Turn it ON if you are using Gemini and it is doing stitching.	❇️	🔧parameter