太史公书变异检测VarScan软件使⽤说明
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华生行为主义VarScan使⽤⽰例，如下：
samtools mpileup -q35 -d8000 -f GBS_A909.fa M008_alignmen_F4.sort.bam >M008_alignmen_F4.sort.mpileup
java -jar VarScan.v2.4.0.jar mpileup2indel M008_alignmen_F4.sort.mpileup --min-var-freq 0 --p-value 0.99 --min-avg-qual 1 --min-coverage 1 --output-vcf 1 > M008_alignmen_F4.sort.
wished得到的⽂件M008_alignmen_F4.sort.的格式如下所⽰：
Tab-delimited SNP calls with the following columns:
Chrom chromosome name
Position position (1-bad)
Ref reference allele at this position
Var variant allele obrved
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PoolCall Cross-sample call using all data (Cons:Cov:Reads1:Reads2:Freq:P-value)
Cons - connsus 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 obrved reads vs expected non-variant
振聋发聩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 rever strand
R2+ = variant supporting reads on forward strand
R2- = variant supporting reads on rever strand
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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 parated by colons:
Cons - connsus 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 obrved reads vs expected non-variant
以下是对varscan2的使⽤说明：
Commands
Three VarScan subcommands will invoke the germline variant calling model. The work with single-sample and multi-sample mpileup input:
mpileup2snp - calls single nucleotide polymorphisms (SNPs)
mpileup2indel - calls inrtions and deletions (indels)
mpileup2cns - calls a connsus 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. U 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 inrtions and deletions (indels)
pileup2cns - calls a connsus 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.
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