How to randomly sample BAM files
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@wdesouza
Last seen 23 months ago
Brazil

Is it possible to randomly sample BAM files using Rsamtools or GenomicAlignments packages? I would like to write a code similar to sample FASTQ files (using ShortRead):

fl <- "path_to_file.fastq"
f <- FastqSampler(fl, n=1e6)
chunk <- yield(f)
close(f)

Thank you.

rsamtools genomicalignments genomicfiles • 2.0k views
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@martin-morgan-1513
Last seen 16 days ago
United States

See GenomicFiles::reduceByYield and REDUCEsampler, including the example at the end of the help page

fl <- system.file(package="Rsamtools", "extdata", "ex1.bam")
bf <- BamFile(fl, yieldSize=1000)
     
yield <- function(x)
    readGAlignments(x,
        param=ScanBamParam(what=c( "qwidth", "mapq" )))
map <- identity
     
## Samples records from successive chunks of aligned reads.
reduceByYield(bf, yield, map, REDUCEsampler(1000, TRUE))

(Normally the first argument to REDUCEsampler() might be, e.g., 1000000)

 

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Thank you Martin, it works.

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