Shore qVar

shore qVar computes consensus sequence, SNPs, indels and CNVs from alignments.

Command line options

Usage: shore qVar OPTIONS

Mandatory
-n STRING		Name (any of species, strain, accession, project or any other ID)
-f STRING		Reference genome sequence from the IndexFolder, *.shore file
-i STRING[,...]		Merged map.list file(s) or shore directories.
-s STRING		Scoring matrix (found in shore/Analysis/scoring_matrix)
-o STRING		AnalysisFolder, will be created.
Assay type
-g		Genomic (turned on by default)
-e		Exome enrichment (or any enrichment) assays
-t		Quantitative sequencing (RNA-seq, ChIP-seq, DNaseI-seq etc.)
Consensus prediction parameters
-c INT	(Default: 1)	Minimum coverage to attempt consensus base calling (Ref or SNP) at a position.
-d INT	(Default: 2)	Minimum allele coverage to attempt indel calling at a position.
-C INT	(Default: 999999)	Maximum coverage to attempt consensus base/indel calling at a position.
-r INT	(Default: 3)	Maximum repetitiveness (average hits) allowed for consensus base/indel calling.
-q INT	(Default: 5)	Minimum base quality (low quality bases are masked before consensus base calling.
-Q INT	(Default: 10)	Minimum consensus base/indel quality for reported calls.
-a FLOAT	(Default: 0.2)	Minimum allele frequency of reported calls.
-A INT	(Default: 2)	Minimum allele read support of reported calls
-b INT	(Default: 4)	Core offset - do not trust the first and last -b positions of an alignment.
Optional input files
-E STRING		Segment wise (e.g. exon) mean coverage file produced by 'shore count'.
Consensus output
-x		No CNV prediction (improves speed; always off for exome or transcriptome seq)
-y		Graphical output of statistics using R.
-v		Do not remove intermediate output files.