Provided by: bedops_2.4.35+dfsg-1_amd64 bug


       convert2bed - manual page for convert2bed 2.4.35+dfsg




              Alex Reynolds


              $ 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=[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


       The full documentation for convert2bed is maintained as a Texinfo manual.  If the info and
       convert2bed programs are properly installed at your site, the command

              info convert2bed

       should give you access to the complete manual.