gffread Filters and/or converts GFF3/GTF2 records

Usage:

gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"]
  [-o "outfile.gff"] [-t "tname"] [-r [["strand"]"chr":]"start".."end" [-R]]
  [-CTVNJMKQAFGUBHZWTOLE] [-w "exons.fa"] [-x "cds.fa"] [-y "tr_cds.fa"]
  [-i "maxintron"]

Options:

-g  full path to a multi-fasta file with the genomic sequences
    for all input mappings, OR a directory with single-fasta files
    (one per genomic sequence, with file names matching sequence names)
-s  <seq_info.fsize> is a tab-delimited file providing this info
    for each of the mapped sequences:
    <seq-name> <seq-length> <seq-description>
    (useful for -A option with mRNA/EST/protein mappings)
-i  discard transcripts having an intron larger than <maxintron>
-r  only show transcripts overlapping coordinate range <start>..<end>
    (on chromosome/contig <chr>, strand <strand> if provided)
-R  for -r option, discard all transcripts that are not fully
    contained within the given range
-U  discard single-exon transcripts
-C  coding only: discard mRNAs that have no CDS feature
-F  full GFF attribute preservation (all attributes are shown)
-G  only parse additional exon attributes from the first exon
    and move them to the mRNA level (useful for GTF input)
-A  use the description field from <seq_info.fsize> and add it
    as the value for a 'descr' attribute to the GFF record

-O  process also non-transcript GFF records (by default non-transcript
    records are ignored)
-V  discard any mRNAs with CDS having in-frame stop codons
-H  for -V option, check and adjust the starting CDS phase
    if the original phase leads to a translation with an
    in-frame stop codon
-B  for -V option, single-exon transcripts are also checked on the
    opposite strand
-N  discard multi-exon mRNAs that have any intron with a non-canonical
    splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
-J  discard any mRNAs that either lack initial START codon
    or the terminal STOP codon, or have an in-frame stop codon
    (only print mRNAs with a fulll, valid CDS)
--no-pseudo: filter out records matching the 'pseudo' keyword

-M/--merge : cluster the input transcripts into loci, collapsing matching
     transcripts (those with the same exact introns and fully contained)
-d <dupinfo> : for -M option, write collapsing info to file <dupinfo>
--cluster-only: same as --merge but without collapsing matching transcripts
-K  for -M option: also collapse shorter, fully contained transcripts
    with fewer introns than the container
-Q  for -M option, remove the containment restriction:
    (multi-exon transcripts will be collapsed if just their introns match,
    while single-exon transcripts can partially overlap (80%))

--force-exons: make sure that the lowest level GFF features are printed as
    "exon" features
-E  expose (warn about) duplicate transcript IDs and other potential
    problems with the given GFF/GTF records
-D  decode url encoded characters within attributes
-Z  merge close exons into a single exon (for intron size<4)
-w  write a fasta file with spliced exons for each GFF transcript
-x  write a fasta file with spliced CDS for each GFF transcript
-W  for -w and -x options, also write for each fasta record the exon
    coordinates projected onto the spliced sequence
-y  write a protein fasta file with the translation of CDS for each record
-L  Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
-m  <chr_replace> is a reference (genomic) sequence replacement table with
    this format:
    <original_ref_ID> <new_ref_ID>
    GFF records on reference sequences that are not found among the
    <original_ref_ID> entries in this file will be filtered out
-o  the "filtered" GFF records will be written to <outfile.gff>
    (use -o- for printing to stdout)
-t  use <trackname> in the second column of each GFF output line
-T  -o option will output GTF format instead of GFF3