readPileup {Rsamtools} | R Documentation

## Import samtools 'pileup' files.

### Description

Import files created by evaluation of samtools' `pileup -cv` command.

### Usage

    readPileup(file, ...)
    ## S4 method for signature 'connection'
    readPileup(file, ..., variant=c("SNP", "indel", "all"))

### Arguments

`file` | The file name, or `connection`, of the pileup output file to be parsed.
`...` | Additional arguments, passed to methods. For instance, specify `variant` for the readPileup,character-method.
`variant` | Type of variant to parse; select one.

### Value

`readPileup` returns a `GRanges` object.

The value returned by `variant="SNP"` or `variant="all"` contains:

space:

  The chromosome names (fastq ids) of the reference sequence

position:

  The nucleotide position (base 1) of the variant.

referenceBase:

  The nucleotide in the reference sequence.

consensusBase;

  The consensus nucleotide, as determined by samtools pileup.

consensusQuality:

  The phred-scaled consensus quality.

snpQuality:

  The phred-scaled SNP quality (probability of the consensus being identical to the reference).

maxMappingQuality:

  The root mean square mapping quality of reads overlapping the site.

coverage:

  The number of reads covering the site.

The value returned by `variant="indel"` contains space, position, reference, consensus, consensusQuality, snpQuality, maxMappingQuality, and coverage fields, and:

alleleOne, alleleTwo

  The first (typically, in the reference sequence) and second allelic variants.

alleleOneSupport, alleleTwoSupport

  The number of reads supporting each allele.

additionalIndels

  The number of additional indels present.

### Author(s)

Sean Davis

### References

http://samtools.sourceforge.net/

### Examples

    fl <- system.file("extdata", "pileup.txt", package="Rsamtools",
                      mustWork=TRUE)
    (res <- readPileup(fl))
    xtabs(~referenceBase + consensusBase, mcols(res))[DNA_BASES,]

    ## Not run: ## uses a pipe, and arguments passed to read.table
    ## three successive piles of 100 records each
    cmd <- "samtools pileup -cvf human_b36_female.fa.gz na19240_3M.bam"
    p <- pipe(cmd, "r")
    snp <- readPileup(p, nrow=100)  # variant="SNP"
    indel <- readPileup(p, nrow=100, variant="indel")
    all <- readPileup(p, nrow=100, variant="all")

    ## End(Not run)

[Package Rsamtools version 2.10.0 Index]