NAME

       gffread  -  GFF/GTF utility providing format conversions, region filtering, FASTA sequence
       extraction

SYNOPSIS

       gffread  <input_gff>  [-g   <genomic_seqs_fasta>   |   <dir>][-s   <seq_info.fsize>]   [-o
       <outfile.gff>]     [-t     <tname>]     [-r     [[<strand>]<chr>:]<start>..<end>     [-R]]
       [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]  [-i  <maxintron>]
       [--sort-by <refseq_list.txt>]

DESCRIPTION

              Filter  and  convert  GFF3/GTF2  records,  extract corresponding sequences etc.  By
              default (i.e. without -O) only process transcripts, ignore other features.

              <input_gff> is a GFF file, use '-' for stdin

OPTIONS

       -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

       -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     attempt to preserve all GFF attributes preservation

       --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)

       --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)

   Clustering:
       -M/--merge : cluster the input transcripts into loci, discarding

              "duplicated"  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)

       -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)

       -w     write a fasta file with spliced exons for each GFF transcript

       -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  and  -x options, write in the FASTA defline the exon coordinates projected
              onto the spliced sequence; for -y option, write transcript attributes in the  FASTA
              defline

       -S     for -y option, use '*' instead of '.' as stop codon translation

       -L     Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)

       -m     <chr_replace>  is  a  name  mapping  table for converting reference sequence names,
              having this  2-column  format:  <original_ref_ID>  <new_ref_ID>  WARNING:  all  GFF
              records  on  reference sequences whose original IDs are not found in the 1st column
              of this table will be discarded!

       -t     use <trackname> in the 2nd column of each GFF/GTF output line

       -o     print the GFF records to <outfile.gff> (those that passed any given  filters).  Use
              -o- to enable printing of to stdout

       -T     for -o, output will be GTF instead of GFF3

       --bed for -o, output BED format instead of GFF3

       --tlf for -o, output "transcript line format" which is like GFF

              but  exons,  CDS  features  and  related  data  are 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>;

       -v,-E expose (warn about) duplicate transcript IDs and other potential

              problems with the given GFF/GTF records

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.