mafRanges

Reference Code backup Executable files

Extract ranges of target (or query) coverage from maf and output as BED 3 (e.g. for processing by featureBits).

Category

Multiple sequence alignments / Conservation

Usage

mafRanges in.maf db out.bed

Manual

db should appear in in.maf alignments as the first part of "db.seqName"-style sequence names. The seqName part will be used as the chrom field in the range printed to out.bed.

Options

  • -otherDb=oDb: Output ranges only for alignments that include oDb. oDB can be comma-separated list.
  • -notAllOGap: Don't include bases for which all other species have a gap.


 

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