```sh
gffread --help
```

gffread v0.12.7. Usage:
gffread [-g <genomic_seqs_fasta> | <dir>] [-s <seq_info.fsize>] 
 [-o <outfile>] [-t <trackname>] [-r [<strand>]<chr>:<start>-<end> [-R]]
 [--jmatch <chr>:<start>-<end>] [--no-pseudo] 
 [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
 [-j ][--ids <IDs.lst> | --nids <IDs.lst>] [--attrs <attr-list>] [-i <maxintron>]
 [--stream] [--bed | --gtf | --tlf] [--table <attrlist>] [--sort-by <ref.lst>]
 [<input_gff>] 

 Filter, convert or cluster GFF/GTF/BED records, extract the sequence of
 transcripts (exon or CDS) and more.
 By default (i.e. without -O) only transcripts are processed, discarding any
 other non-transcript features. Default output is a simplified GFF3 with only
 the basic attributes.
 
Options:
 --ids discard records/transcripts if their IDs are not listed in <IDs.lst>
 --nids discard records/transcripts if their IDs are listed in <IDs.lst>
 -i   discard transcripts having an intron larger than <maxintron>
 -l   discard transcripts shorter than <minlen> bases
 -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
 --jmatch only output transcripts matching the given junction
 -U   discard single-exon transcripts
 -C   coding only: discard mRNAs that have no CDS features
 --nc non-coding only: discard mRNAs that have CDS features
 --ignore-locus : discard locus features and attributes found in the input
 -A   use the description field from <seq_info.fsize> and add it
      as the value for a 'descr' attribute to the GFF record
 -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)
Sorting: (by default, chromosomes are kept in the order they were found)
 --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
 --sort-by : sort the reference sequences by the order in which their
      names are given in the <refseq.lst> file
Misc options: 
 -F   keep all GFF attributes (for non-exon features)
 --keep-exon-attrs : for -F option, do not attempt to reduce redundant
      exon/CDS attributes
 -G   do not keep exon attributes, move them to the transcript feature
      (for GFF3 output)
 --attrs <attr-list> only output the GTF/GFF attributes listed in <attr-list>
    which is a comma delimited list of attribute names to
 --keep-genes : in transcript-only mode (default), also preserve gene records
 --keep-comments: for GFF3 input/output, try to preserve comments
 -O   process other non-transcript GFF records (by default non-transcript
      records are ignored)
 -V   discard any mRNAs with CDS having in-frame stop codons (requires -g)
 -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 (requires -g)
 -P   add transcript level GFF attributes about the coding status of each
      transcript, including partialness or in-frame stop codons (requires -g)
 --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
      that have CDS features
 --adj-stop stop codon adjustment: enables -P and performs automatic
      adjustment of the CDS stop coordinate if premature or downstream
 -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
      (i.e. only print mRNAs with a complete CDS)
 --no-pseudo: filter out records matching the 'pseudo' keyword
 --in-bed: input should be parsed as BED format (automatic if the input
           filename ends with .bed*)
 --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
           features (see --tlf option below); automatic if the input
           filename ends with .tlf)
 --stream: fast processing of input GFF/BED transcripts as they are received
           ((no sorting, exons must be grouped by transcript in the input data)
Clustering:
 -M/--merge : cluster the input transcripts into loci, discarding
      "redundant" transcripts (those with the same exact introns
      and fully contained or equal boundaries)
 -d <dupinfo> : for -M option, write duplication info to file <dupinfo>
 --cluster-only: same as -M/--merge but without discarding any of the
      "duplicate" transcripts, only create "locus" features
 -K   for -M option: also discard as redundant the shorter, fully contained
       transcripts (intron chains matching a part of the container)
 -Q   for -M option, no longer require boundary containment when assessing
      redundancy (can be combined with -K); only introns have to match for
      multi-exon transcripts, and >=80% overlap for single-exon transcripts
 -Y   for -M option, enforce -Q but also discard overlapping single-exon 
      transcripts, even on the opposite strand (can be combined with -K)
Output options:
 --force-exons: make sure that the lowest level GFF features are considered
       "exon" features
 --gene2exon: for single-line genes not parenting any transcripts, add an
       exon feature spanning the entire gene (treat it as a transcript)
 --t-adopt:  try to find a parent gene overlapping/containing a transcript
       that does not have any explicit gene Parent
 -D    decode url encoded characters within attributes
 -Z    merge very close exons into a single exon (when intron size<4)
 -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)
 -j    output the junctions and the corresponding transcripts
 -w    write a fasta file with spliced exons for each transcript
 --w-add <N> for the -w option, extract additional <N> bases
       both upstream and downstream of the transcript boundaries
 --w-nocds for -w, disable the output of CDS info in the FASTA file
 -x    write a fasta file with spliced CDS for each GFF transcript
 -y    write a protein fasta file with the translation of CDS for each record
 -W    for -w, -x and -y options, write in the FASTA defline all the exon
       coordinates projected onto the spliced sequence;
 -S    for -y option, use '*' instead of '.' as stop codon translation
 -L    Ensembl GTF to GFF3 conversion, adds version to IDs
 -m    <chr_replace> is a name mapping table for converting reference 
       sequence names, having this 2-column format:
       <original_ref_ID> <new_ref_ID>
 -t    use <trackname> in the 2nd column of each GFF/GTF output line
 -o    write the output records into <outfile> instead of stdout
 -T    main output will be GTF instead of GFF3
 --bed output records in BED format instead of default GFF3
 --tlf output "transcript line format" which is like GFF
       but with exons and CDS related features stored as GFF 
       attributes in the transcript feature line, like this:
         exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords> 
       <exons> is a comma-delimited list of exon_start-exon_end coordinates;
       <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>
 --table output a simple tab delimited format instead of GFF, with columns
       having the values of GFF attributes given in <attrlist>; special
       pseudo-attributes (prefixed by @) are recognized:
       @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, 
       @cds, @covlen, @cdslen
       If any of -w/-y/-x FASTA output files are enabled, the same fields
       (excluding @id) are appended to the definition line of corresponding
       FASTA records
 -v,-E expose (warn about) duplicate transcript IDs and other potential
       problems with the given GFF/GTF records