变异检测VarScan软件使用说明
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
Commands
Three VarScan subcommands will invoke the germline variant calling model. These work with single-sample and multi-sample mpileup input:mpileup2snp - calls single nucleotide polymorphisms (SNPs) mpileup2indel - calls insertions and deletions (indels) mpileup2cns - calls a consensus genotype (reference, SNP, or indel)
The first two (mpileup2snp and mpileup2indel) report *only* positions at which a variant of the given type (SNP and indel) was called. The third command (mpileup2cns) reports all positions that met the miniumum coverage, or (with the -v parameter), all positions at which a SNP or an indel was called. Use the --output-vcf 1 argument to get VCF 4.1 output. (能够得到vcf格式的文件)
The following commands still work, but only with single-sample pileup and they do NOT include full VCF output support.
pileup2snp - calls single nucleotide polymorphisms (SNPs) pileup2indel - calls insertions and deletions (indels) pileup2cns - calls a consensus genotype (reference, SNP, or indel)
The first two (pileup2snp and pileup2indel) report *only* positions at which a variant of the given type (SNP and indel) was called. The third command (pileup2cns) reports all positions that met the miniumum coverage, or (with the -v parameter), all positions at which a SNP or an indel was called.