Category
Variant Analysis
Usage
java -jar VarScan.jar pileup2indel [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 indel 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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