convert2bed1

Overview

convert2bed

version:

2.4.41

author:

Alex Reynolds

Usage:

$ convert2bed --input=fmt [--output=fmt] [options] < input > output

Convert BAM, GFF, GTF, GVF, PSL, RepeatMasker (OUT), SAM, VCF and WIG genomic formats to BED or BEDOPS Starch (compressed BED)

Input can be a regular file or standard input piped in using the hyphen character ('-'):

$ some_upstream_process ... | convert2bed --input=fmt - > output

Input (required):

--input=[bam|gff|gtf|gvf|psl|rmsk|sam|vcf|wig] (-i <fmt>)

Genomic format of input file (required)

Output:

--output=[bed|starch] (-o <fmt>)

Format of output file, either BED or BEDOPS Starch (optional, default is BED)

Other processing options:

--do-not-sort (-d)

Do not sort BED output with sort-bed (not compatible with --output=starch)

--max-mem=<value> (-m <val>)

Sets aside <value> memory for sorting BED output. For example, <value> can be 8G, 8000M or 8000000000 to specify 8 GB of memory (default is 2G)

--sort-tmpdir=<dir> (-r <dir>)

Optionally sets [dir] as temporary directory for sort data, when used in conjunction with --max-mem=[value], instead of the host's operating system default temporary directory

--starch-bzip2 (-z)

Used with --output=starch, the compressed output explicitly applies the bzip2 algorithm to compress intermediate data (default is bzip2)

--starch-gzip (-g)

Used with --output=starch, the compressed output applies gzip compression on intermediate data

--starch-note="xyz..." (-e "xyz...")

Used with --output=starch, this adds a note to the Starch archive metadata

--help | --help[-bam|-gff|-gtf|-gvf|-psl|-rmsk|-sam|-vcf|-wig] (-h | -h <fmt>)

Show general help message (or detailed help for a specified input format)

--version (-w)

Show application version