Category

Variant Analysis


Usage

java -jar VarScan.jar pileup2cns [pileup file] OPTIONS


Manual

OPTIONS:

--min-coverage  Minimum read depth at a position to make a call [8]
--min-reads2    Minimum supporting reads at a position to call variants [2]
--min-avg-qual  Minimum base quality at a position to count a read [15]
--min-var-freq  Minimum variant allele frequency threshold [0.01]
--p-value       Default p-value threshold for calling variants [99e-02]

OUTPUT

Tab-delimited consensus calls with the following columns:

Chrom        chromosome name
Position    position (1-based)
Ref        reference allele at this position
Cons        Consensus genotype of sample; */(var) indicates heterozygous
Reads1        reads supporting reference allele
Reads2        reads supporting variant allele
VarFreq        frequency of variant allele by read count
Strands1    strands on which reference allele was observed
Strands2    strands on which variant allele was observed
Qual1        average base quality of reference-supporting read bases
Qual2        average base quality of variant-supporting read bases
Pvalue        Significance of variant read count vs. expected baseline error
MapQual1    Average map quality of ref reads (only useful if in pileup)
MapQual2    Average map quality of var reads (only useful if in pileup)
Reads1Plus    Number of reference-supporting reads on + strand
Reads1Minus    Number of reference-supporting reads on - strand
Reads2Plus    Number of variant-supporting reads on + strand
Reads2Minus    Number of variant-supporting reads on - strand
VarAllele    Most frequent non-reference allele observed


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