$ bedtools sample
Tool: bedtools sample (aka sampleFile)
Version: v2.30.0
Summary: Take sample of input file(s) using reservoir sampling algorithm.
Usage: bedtools sample [OPTIONS] -i <bed/gff/vcf/bam>
WARNING: The current sample algorithm will hold all requested sample records in memory prior to output.
The user must ensure that there is adequate memory for this.
Options:
-n The number of records to generate.
- Default = 1,000,000.
- (INTEGER)
-seed Supply an integer seed for the shuffling.
- By default, the seed is chosen automatically.
- (INTEGER)
-ubam Write uncompressed BAM output. Default writes compressed BAM.
-s Require same strandedness. That is, only give records
that have the same strand. Use '-s forward' or '-s reverse'
for forward or reverse strand records, respectively.
- By default, records are reported without respect to strand.
-header Print the header from the input file prior to results.
-bed If using BAM input, write output as BED.
-header Print the header from the A file prior to results.
-nobuf Disable buffered output. Using this option will cause each line
of output to be printed as it is generated, rather than saved
in a buffer. This will make printing large output files
noticeably slower, but can be useful in conjunction with
other software tools and scripts that need to process one
line of bedtools output at a time.
-iobuf Specify amount of memory to use for input buffer.
Takes an integer argument. Optional suffixes K/M/G supported.
Note: currently has no effect with compressed files.
arq5x
commented
2 years ago
I didn't even know the "sample" feature existed, relying in part on this list: https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html