Man page - convert2bed(1)

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CONVERT2BED(1)

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CONVERT2BED(1)

convert2bed - manual page for convert2bed 2.4.41+dfsg

convert2bed

: 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>)

--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>)

--version (-w)