bam2stat | R Documentation |
This function takes as an input aligned reads in BAM and exports some useful statistics like depth of coverage and percentage of genome being coverged by reads.
bam2stat(
bamfile,
bamindex = paste0(bamfile, ".bai"),
chromosomes = NULL,
chunkSize = NULL,
min.mapq = 10,
filt.flag = 3328,
filt.alt = FALSE
)
bamfile |
Bamfile with aligned reads. |
bamindex |
Bam-index file with or without the .bai ending. If this file does not exist it will be created and a warning is issued. |
chromosomes |
If only a subset of the chromosomes should be binned, specify them here. |
chunkSize |
Set for big BAMs to process them in smaller chunks. |
min.mapq |
Minimum mapping quality when importing from BAM files. |
filt.flag |
Filter out reads with a given flag. |
filt.alt |
Set to |
data.frame
David Porubsky
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