Mercurial > repos > iuc > bcftools_convert_to_vcf

annotate test-data/csq.gff3 @ 21:2b3ce2abc747 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 868f4386992de55d25da197660a43a913a09c8df
author iuc
date Wed, 14 Aug 2024 16:33:43 +0000
parents 7b50ab23976c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
1 ##gff-version 3
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
2 #! This file shows which fields are used and required by `bcftools +csq`. It is a trimmed version
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
3 #! of the GFF3 format, see an example of the full format here
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
4 #! ftp://ftp.ensembl.org/pub/grch37/release-84/gff3/homo_sapiens/
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
5 #!
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
6 ###
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
7 1 . gene 90 200 . + . ID=gene:ENSG00000000001;Name=XYZ;biotype=protein_coding
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
8 1 . transcript 90 200 . + . ID=transcript:ENST00000000001;Parent=gene:ENSG00000000001;biotype=protein_coding
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
9 1 . exon 90 110 . + . Parent=transcript:ENST00000000001
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
10 1 . five_prime_UTR 90 98 . + . Parent=transcript:ENST00000000001
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
11 1 . CDS 99 110 . + 1 Parent=transcript:ENST00000000001
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
12 1 . exon 120 130 . + . Parent=transcript:ENST00000000001
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
13 1 . CDS 120 130 . + 1 Parent=transcript:ENST00000000001
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
14 1 . exon 140 150 . + . Parent=transcript:ENST00000000001
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
15 1 . CDS 140 150 . + 2 Parent=transcript:ENST00000000001
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
16 1 . exon 160 200 . + . Parent=transcript:ENST00000000001
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
17 1 . CDS 160 171 . + 0 Parent=transcript:ENST00000000001
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
18 1 . three_prime_UTR 172 200 . + . Parent=transcript:ENST00000000001
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
19 2 . gene 80 200 . - . ID=gene:ENSG00000000002;Name=ABC;biotype=protein_coding
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
20 2 . transcript 80 200 . - . ID=transcript:ENST00000000002;Parent=gene:ENSG00000000002;biotype=protein_coding
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
21 2 . exon 80 110 . - . Parent=transcript:ENST00000000002
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
22 2 . three_prime_UTR 80 98 . - . Parent=transcript:ENST00000000002
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
23 2 . CDS 99 110 . - 0 Parent=transcript:ENST00000000002
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
24 2 . exon 120 130 . - . Parent=transcript:ENST00000000002
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
25 2 . CDS 120 130 . - 2 Parent=transcript:ENST00000000002
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
26 2 . exon 140 150 . - . Parent=transcript:ENST00000000002
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
27 2 . CDS 140 150 . - 1 Parent=transcript:ENST00000000002
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
28 2 . exon 160 200 . - . Parent=transcript:ENST00000000002
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
29 2 . CDS 160 171 . - 1 Parent=transcript:ENST00000000002
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
30 2 . five_prime_UTR 172 200 . - . Parent=transcript:ENST00000000002
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
31 3 . lincRNA_gene 20 50 . - . ID=gene:ENSG00000000004;Name=mir-007;biotype=lincRNA
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
32 3 . lincRNA 20 50 . - . ID=transcript:ENSG00000000004;Parent=gene:ENSG00000000004;biotype=lincRNA
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
33 3 . gene 100 200 . - . ID=gene:ENSG00000000003;Name=QWRTY;biotype=protein_coding
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
34 3 . transcript 100 200 . - . ID=transcript:ENST00000000003;Parent=gene:ENSG00000000003;biotype=protein_coding
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
35 3 . exon 100 110 . - . Parent=transcript:ENST00000000003
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
36 3 . three_prime_UTR 100 105 . - . Parent=transcript:ENST00000000003
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
37 3 . CDS 106 110 . - 0 Parent=transcript:ENST00000000003
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
38 3 . exon 160 200 . - . Parent=transcript:ENST00000000003
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
39 3 . CDS 160 171 . - 0 Parent=transcript:ENST00000000003
7b50ab23976c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
40 3 . five_prime_UTR 172 200 . - . Parent=transcript:ENST00000000003