Calculation of basic alignments statistics

Description

Calculates some basic alignment statistics for given bam files.

Usage

getAlignmentQuality(bamFile, verbose = FALSE, mc.cores = 1)

Arguments

Details

The given bam files should have marked duplicates and not uniquely mapped reads should have a quality value of 0. In detail, this function returns a data frame with the following columns:

Sample

File name without path and suffix

HeaderID

ID field from bam header, if available

HeaderSampleID

SM field from bam header, if available

HeaderLibraryID

LB field from bam header, if available

TotalReads

Total number of reads in bam file

MappedReads

Number of mapped Reads

MappedReadsRel

MappedReads/TotalReads

UniquelyMappedReads

Number of mapped reads with mapping quality larger 0

UniquelyMappedReadsRel

UniquelyMappedReads/MappedReads

UniquelyMappedUniqueReads

Number of non duplicated mapped reads with mapping quality larger 0

UniquelyMappedUniqueReadsRel

UniquelyMappedUniqueReads/MappedReads

NonRedundantFraction

UniquelyMappedUniqueReads/UniquelyMappedReads

QualMean

Mean mapping quality of all uniquely mapped unique reads

QualSd

Standard deviation of the mapping quality of all uniquely mapped unique reads

Quantile0

0% quantileof the mapping quality of all uniquely mapped unique reads

Quantile25

25% quantile of the mapping quality of all uniquely mapped unique reads

Quantile50

50% quantile of the mapping quality of all uniquely mapped unique reads

Quantile75

75% quantile of the mapping quality of all uniquely mapped unique reads

Quantile100

100% quantile of the mapping quality of all uniquely mapped unique reads

Path

Full path and file name as given in argument bamFile

Value

Returns a data frame with one row for each given bam file and the columns as listed in the details section.

Author(s)

Hans-Ulrich Klein (hklein@broadinstitute.org)

Examples

## Not run: getAlignmentQuality("myFile.bam")

Results