Mapping quality control

Check the mapping rate, PCR duplication rate, and mitochondria reads contamination.

bamQC(
  bamfile,
  index = bamfile,
  mitochondria = "chrM",
  outPath = sub(".bam", ".clean.bam", basename(bamfile)),
  doubleCheckDup = FALSE
)

Arguments

bamfile	character(1). File name of bam.
index	character(1). File name of index file.
mitochondria	character(1). Sequence name of mitochondria.
outPath	character(1). File name of cleaned bam.
doubleCheckDup	logical(1). Double check duplicates or not if there is no tags for that.

Value

A list of quality summary.

Author

Jianhong Ou

Examples

bamfile <- system.file("extdata", "GL1.bam", package="ATACseqQC")
bamQC(bamfile, outPath=NULL)
#> $totalQNAMEs
#> [1] 44357
#> 
#> $duplicateRate
#> [1] 0
#> 
#> $mitochondriaRate
#> [1] 0
#> 
#> $properPairRate
#> [1] 0.9815136
#> 
#> $unmappedRate
#> [1] 0
#> 
#> $hasUnmappedMateRate
#> [1] 0
#> 
#> $notPassingQualityControlsRate
#> [1] 0
#> 
#> $nonRedundantFraction
#> [1] 0.9398066
#> 
#> $PCRbottleneckCoefficient_1
#> [1] 0.9689694
#> 
#> $PCRbottleneckCoefficient_2
#> [1] 31.22622
#> 
#> $MAPQ
#>    Var1  Freq
#> 1    21    44
#> 2    22    12
#> 3    23   536
#> 4    24   606
#> 5    25    14
#> 6    26    10
#> 7    27     4
#> 8    30  1682
#> 9    31   780
#> 10   32   238
#> 11   34   244
#> 12   35   118
#> 13   36    44
#> 14   37    62
#> 15   38    64
#> 16   39    34
#> 17   40  2076
#> 18   42 82146
#> 
#> $idxstats
#>    seqnames seqlength mapped unmapped
#> 1      chr1 249250621  88714        0
#> 2      chr2 243199373      0        0
#> 3      chr3 198022430      0        0
#> 4      chr4 191154276      0        0
#> 5      chr5 180915260      0        0
#> 6      chr6 171115067      0        0
#> 7      chr7 159138663      0        0
#> 8      chr8 146364022      0        0
#> 9      chr9 141213431      0        0
#> 10    chr10 135534747      0        0
#> 11    chr11 135006516      0        0
#> 12    chr12 133851895      0        0
#> 13    chr13 115169878      0        0
#> 14    chr14 107349540      0        0
#> 15    chr15 102531392      0        0
#> 16    chr16  90354753      0        0
#> 17    chr17  81195210      0        0
#> 18    chr18  78077248      0        0
#> 19    chr19  59128983      0        0
#> 20    chr20  63025520      0        0
#> 21    chr21  48129895      0        0
#> 22    chr22  51304566      0        0
#> 23     chrX 155270560      0        0
#> 24     chrY  59373566      0        0
#> 25     chrM     16571      0        0
#>