<p>I would consider the description there a bug. The <code>filter</code> is actually the strand, <code>strand</code> is the frame, <code>group</code> is the attribute, and <code>attribute</code> does nothing. These are really meant to be the 9 columns.</p>

<p><strong>Edit</strong>: There's a <a href="https://github.com/lh3/bioawk/issues/16" rel="nofollow noreferrer">bug report</a> related to this.</p>

<p><strong>Edit 2</strong>: I've made <a href="https://github.com/lh3/bioawk/pull/21" rel="nofollow noreferrer">a pull request</a> to clarify this and fix the aforementioned bug report.</p>

<p><strong>Edit 3</strong>: I realized that I never directly answered the title of your question (<em>mea culpa</em>). bioawk itself will work with gff, gff3, or gtf files. It really is just treating them as tab-separated files with named columns (this is surprisingly convenient, since it's a PITA to remember what column does what).</p>

<p><strong>Edit 4</strong>: The PR has been merged. If you install from github then you'll see corrected field names.</p>

CC BY-SA 3.0
2017-06-12T18:00:21.667Z
2017-06-13T07:02:39.247Z
2017-06-13T07:02:39.247Z
Devon Ryan
<p>I was wondering if I could use the gff parsing capability of bioawk to facilitate the parsing of gtf files, and I looked at the following help message:</p>

<pre><code>$ bioawk -c help
bed:
    1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts 
sam:
    1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual 
vcf:
    1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info 
gff:
    1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute 
fastx:
    1:name 2:seq 3:qual 4:comment 
</code></pre>

<p>I see that there are 10 fields defined for gff parsing.</p>

<p>However, when I look at the pages for gtf and gff in the ensembl website (<a href="http://www.ensembl.org/info/website/upload/gff.html" rel="nofollow noreferrer">gff/gtf</a> and <a href="http://www.ensembl.org/info/website/upload/gff3.html" rel="nofollow noreferrer">gff3</a>), all have 9 fields.</p>

<p>I'm curious about these "filter" and "group" fields. What are they meant for? Are they extracted from some of the columns mentioned in the above pages?</p>

<file-formats><gff3><gtf><bioawk>
What kind of "gff" format does bioawk parse?
# What kind of "gff" format does bioawk parse?

(Asked by: username_0 on 2017-06-12)

I was wondering if I could use the gff parsing capability of bioawk to facilitate the parsing of gtf files, and I looked at the following help message:
$ bioawk -c help
bed:
    1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts 
sam:
    1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual 
vcf:
    1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info 
gff:
    1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute 
fastx:
    1:name 2:seq 3:qual 4:comment 

I see that there are 10 fields defined for gff parsing.
However, when I look at the pages for gtf and gff in the ensembl website (gff/gtf and gff3), all have 9 fields.
I'm curious about these "filter" and "group" fields. What are they meant for? Are they extracted from some of the columns mentioned in the above pages?

**Tags:** file-formats, gff3, gtf, bioawk

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## 1 answers

### Answer by username_1 on 2017-06-12. Score: 5 | Accepted answer

I would consider the description there a bug. The `filter` is actually the strand, `strand` is the frame, `group` is the attribute, and `attribute` does nothing. These are really meant to be the 9 columns.

**Edit**: There's a [bug report](https://github.com/lh3/bioawk/issues/16) related to this.

**Edit 2**: I've made [a pull request](https://github.com/lh3/bioawk/pull/21) to clarify this and fix the aforementioned bug report.

**Edit 3**: I realized that I never directly answered the title of your question (*mea culpa*). bioawk itself will work with gff, gff3, or gtf files. It really is just treating them as tab-separated files with named columns (this is surprisingly convenient, since it's a PITA to remember what column does what).

**Edit 4**: The PR has been merged. If you install from github then you'll see corrected field names.


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