This command makes consensus calls (SNP/Indel/Reference) from a mpileup file based on user-defined parameters: USAGE: java -jar VarScan.jar mpileup2cns [mpileup file] OPTIONS
mpileup file - The SAMtools mpileup file
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]
--min-freq-for-hom Minimum frequency to call homozygote [0.75]
--p-value Default p-value threshold for calling variants [99e-02]
--strand-filter Ignore variants with >90% support on one strand [1]
--output-vcf If set to 1, outputs in VCF format
--variants Report only variant (SNP/indel) positions (mpileup2cns only) [0]
OUTPUT
Tab-delimited SNP calls with the following columns:
Chrom chromosome name
Position position (1-based)
Ref reference allele at this position
Var variant allele observed
PoolCall Cross-sample call using all data (Cons:Cov:Reads1:Reads2:Freq:P-value)
Cons - consensus genotype in IUPAC format
Cov - total depth of coverage
Reads1 - number of reads supporting reference
Reads2 - number of reads supporting variant
Freq - the variant allele frequency by read count
P-value - FET p-value of observed reads vs expected non-variant
StrandFilt Information to look for strand bias using all reads, format R1+:R1-:R2+:R2-:pval
R1+ = reference supporting reads on forward strand
R1- = reference supporting reads on reverse strand
R2+ = variant supporting reads on forward strand
R2- = variant supporting reads on reverse strand
pval = FET p-value for strand distribution, R1 versus R2
SamplesRef Number of samples called reference (wildtype)
SamplesHet Number of samples called heterozygous-variant
SamplesHom Number of samples called homozygous-variant
SamplesNC Number of samples not covered / not called
SampleCalls The calls for each sample in the mpileup, space-delimited
Each sample has six values separated by colons:
Cons - consensus genotype in IUPAC format
Cov - total depth of coverage
Reads1 - number of reads supporting reference
Reads2 - number of reads supporting variant
Freq - the variant allele frequency by read count
P-value - FET p-value of observed reads vs expected non-variant
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