unmapped_read: Extract unmapped reads with a mapped mate from a bam file

View source: R/fasta-utils.R

unmapped_readR Documentation

Extract unmapped reads with a mapped mate from a bam file

Description

This function extracts all unmapped reads with a mate that overlaps with a set of query genomic intervals. Internally, this function uses scanBam to scan the bam files. In our application, we typically create a bam file containing only mapped-unmapped read pairs as this greatly reduces the size of the bam file to query. In particular, we create a bam file with the following set of flags:

Usage

unmapped_read(
  bam.file,
  query,
  yield_size = 1e+06,
  maxgap = 500,
  what = scanBamWhat()
)

Arguments

bam.file

character-string providing complete path to BAM file

query

a GRanges representation of genomic intervals to query for a mapped read with an unmapped mate. For example, a set of rearrangement intervals.

yield_size

the number of reads to extract from the bam file at once using scanBam

maxgap

the gap allowed between the query interval and the mapped read to consider the two intervals overlapping

what

a character vector of fields to keep from the bam file. Defaults to scanBamWhat().

Details

samtools view -b -f 4 -F 8 $input > "unmapped-mapped/${input}"

The GRanges object returned by this function includes the sequence of the reads so that the sequences can be subsequently written to disk in fasta format and realigned with a local alignment algorithm such as BLAT that allows for split read alignments.

Value

a GRanges object of mapped reads with unmapped mates.

See Also

See scanBam for scanning a bam file for reads matching a set of flags. See fasta_unmapped for writting these sequences to disk in fasta format.

Examples

extdata <- system.file("extdata", package="svbams")
bam <- file.path(extdata, "cgov44t_revised.bam")
region <- GRanges(seqnames = "chr8",
ranges = IRanges(start = 128691748, end = 128692097))
unmapped_read(bam.file = bam, query = region, yield_size = 1e6)

cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.