GtfLiftOver

Last commit

LiftOver GTF file.

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar gtfliftover  [options] Files

Usage: gtfliftover [options] Files
  Options:
  * -f, --chain
      LiftOver file.
    -x, --failed
      write  failing the liftOver here. Optional.
    -H, --header
      include gtf header
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -m, --minmatch
      lift over min-match.
      Default: 0.95
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

gtf
liftover

Creation Date

20190823

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/gtf/GtfLiftOver.java

Contribute

Issue Tracker: http://github.com/lindenb/jvarkit/issues
Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite gtfliftover ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

$ gunzip -c ~/data/homo_sapiens.GRCh38.Regulatory_Build.regulatory_features.20190329.gff.gz | grep ^X | head 
X   Regulatory_Build    CTCF_binding_site   100072201   100072600   .   .   .   ID=CTCF_binding_site:ENSR00000911312;bound_end=100072600;bound_start=100072201;description=CTCF binding site;feature_type=CTCF Binding Site
X   Regulatory_Build    CTCF_binding_site   100076001   100076400   .   .   .   ID=CTCF_binding_site:ENSR00000911313;bound_end=100076400;bound_start=100076001;description=CTCF binding site;feature_type=CTCF Binding Site
X   Regulatory_Build    CTCF_binding_site   100080601   100080800   .   .   .   ID=CTCF_binding_site:ENSR00000911314;bound_end=100080800;bound_start=100080601;description=CTCF binding site;feature_type=CTCF Binding Site
X   Regulatory_Build    CTCF_binding_site   100099201   100099400   .   .   .   ID=CTCF_binding_site:ENSR00000911321;bound_end=100099400;bound_start=100099201;description=CTCF binding site;feature_type=CTCF Binding Site
X   Regulatory_Build    CTCF_binding_site   10015601    10016000    .   .   .   ID=CTCF_binding_site:ENSR00000901123;bound_end=10016000;bound_start=10015601;description=CTCF binding site;feature_type=CTCF Binding Site
X   Regulatory_Build    CTCF_binding_site   10018001    10018400    .   .   .   ID=CTCF_binding_site:ENSR00000901124;bound_end=10018400;bound_start=10018001;description=CTCF binding site;feature_type=CTCF Binding Site
X   Regulatory_Build    CTCF_binding_site   100185401   100185800   .   .   .   ID=CTCF_binding_site:ENSR00000911326;bound_end=100185800;bound_start=100185401;description=CTCF binding site;feature_type=CTCF Binding Site
X   Regulatory_Build    CTCF_binding_site   10021601    10021800    .   .   .   ID=CTCF_binding_site:ENSR00000901125;bound_end=10021800;bound_start=10021601;description=CTCF binding site;feature_type=CTCF Binding Site
X   Regulatory_Build    CTCF_binding_site   100351201   100351400   .   .   .   ID=CTCF_binding_site:ENSR00001161915;bound_end=100351400;bound_start=100351201;description=CTCF binding site;feature_type=CTCF Binding Site
X   Regulatory_Build    CTCF_binding_site   100368001   100368800   .   .   .   ID=CTCF_binding_site:ENSR00000342428;bound_end=100368800;bound_start=100368001;description=CTCF binding site;feature_type=CTCF Binding Site

$ java -jar dist/gtfliftover.jar -x jeter.boum -f ../htsjdk/src/test/resources/htsjdk/samtools/liftover/hg18ToHg19.over.chain ~/data/homo_sapiens.GRCh38.Regulatory_Build.regulatory_features.20190329.gff.gz  2> /dev/null | head
chrX    Regulatory_Build    CTCF_binding_site   100185545   100185944   .   .   .   ID=CTCF_binding_site:ENSR00000911312;bound_end=100072600;bound_start=100072201;description=CTCF binding site;feature_type=CTCF Binding Site
chrX    Regulatory_Build    CTCF_binding_site   100189345   100189744   .   .   .   ID=CTCF_binding_site:ENSR00000911313;bound_end=100076400;bound_start=100076001;description=CTCF binding site;feature_type=CTCF Binding Site
chrX    Regulatory_Build    CTCF_binding_site   100193945   100194144   .   .   .   ID=CTCF_binding_site:ENSR00000911314;bound_end=100080800;bound_start=100080601;description=CTCF binding site;feature_type=CTCF Binding Site
chrX    Regulatory_Build    CTCF_binding_site   100212545   100212744   .   .   .   ID=CTCF_binding_site:ENSR00000911321;bound_end=100099400;bound_start=100099201;description=CTCF binding site;feature_type=CTCF Binding Site
chrX    Regulatory_Build    CTCF_binding_site   10055601    10056000    .   .   .   ID=CTCF_binding_site:ENSR00000901123;bound_end=10016000;bound_start=10015601;description=CTCF binding site;feature_type=CTCF Binding Site
chrX    Regulatory_Build    CTCF_binding_site   10058001    10058400    .   .   .   ID=CTCF_binding_site:ENSR00000901124;bound_end=10018400;bound_start=10018001;description=CTCF binding site;feature_type=CTCF Binding Site
chrX    Regulatory_Build    CTCF_binding_site   100298745   100299144   .   .   .   ID=CTCF_binding_site:ENSR00000911326;bound_end=100185800;bound_start=100185401;description=CTCF binding site;feature_type=CTCF Binding Site
chrX    Regulatory_Build    CTCF_binding_site   10061601    10061800    .   .   .   ID=CTCF_binding_site:ENSR00000901125;bound_end=10021800;bound_start=10021601;description=CTCF binding site;feature_type=CTCF Binding Site
chrX    Regulatory_Build    CTCF_binding_site   100464545   100464744   .   .   .   ID=CTCF_binding_site:ENSR00001161915;bound_end=100351400;bound_start=100351201;description=CTCF binding site;feature_type=CTCF Binding Site
chrX    Regulatory_Build    CTCF_binding_site   100481345   100482144   .   .   .   ID=CTCF_binding_site:ENSR00000342428;bound_end=100368800;bound_start=100368001;description=CTCF binding site;feature_type=CTCF Binding Site

when the GTF contains a gene, all sub-section MUST be re-mapped.

$ gunzip -c ~/src/jvarkit-git/src/test/resources/Homo_sapiens.GRCh37.87.gtf.gz | head
22  ensembl_havana  exon    41697526    41697776    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000352645"; transcript_version "4"; exon_number "1"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14013"; havana_transcript "OTTHUMT00000320696"; havana_transcript_version "1"; exon_id "ENSE00001307363"; exon_version "4"; tag "basic";
22  ensembl_havana  five_prime_utr  41697526    41697776    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000352645"; transcript_version "4"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14013"; havana_transcript "OTTHUMT00000320696"; havana_transcript_version "1"; tag "basic";
22  ensembl_havana  gene    41697526    41756151    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding";
22  ensembl_havana  transcript  41697526    41756151    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000352645"; transcript_version "4"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14013"; havana_transcript "OTTHUMT00000320696"; havana_transcript_version "1"; tag "basic";
22  havana  exon    41697719    41697776    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000486331"; transcript_version "1"; exon_number "1"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-002"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000320697"; havana_transcript_version "1"; exon_id "ENSE00001942555"; exon_version "1";
22  havana  transcript  41697719    41732847    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000486331"; transcript_version "1"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-002"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000320697"; havana_transcript_version "1";
22  ensembl_havana  exon    41716659    41716717    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000352645"; transcript_version "4"; exon_number "2"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14013"; havana_transcript "OTTHUMT00000320696"; havana_transcript_version "1"; exon_id "ENSE00003628979"; exon_version "1"; tag "basic";
22  ensembl_havana  five_prime_utr  41716659    41716664    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000352645"; transcript_version "4"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14013"; havana_transcript "OTTHUMT00000320696"; havana_transcript_version "1"; tag "basic";
22  havana  exon    41716659    41716717    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000486331"; transcript_version "1"; exon_number "2"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-002"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000320697"; havana_transcript_version "1"; exon_id "ENSE00003530265"; exon_version "1";
22  ensembl CDS 41716665    41716717    .   +   0   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000351589"; transcript_version "4"; exon_number "1"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14013"; protein_id "ENSP00000263243"; protein_version "5"; tag "basic";

$ java -jar dist/gtfliftover.jar -f ../htsjdk/src/test/resources/htsjdk/samtools/liftover/hg18ToHg19.over.chain ~/src/jvarkit-git/src/test/resources/Homo_sapiens.GRCh37.87.gtf.gz  --header 2> /dev/null  | head
chr22   ensembl_havana  exon    43367582    43367832    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000352645"; transcript_version "4"; exon_number "1"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14013"; havana_transcript "OTTHUMT00000320696"; havana_transcript_version "1"; exon_id "ENSE00001307363"; exon_version "4"; tag "basic";
chr22   ensembl_havana  five_prime_utr  43367582    43367832    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000352645"; transcript_version "4"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14013"; havana_transcript "OTTHUMT00000320696"; havana_transcript_version "1"; tag "basic";
chr22   ensembl_havana  gene    43367582    43426207    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding";
chr22   ensembl_havana  transcript  43367582    43426207    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000352645"; transcript_version "4"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14013"; havana_transcript "OTTHUMT00000320696"; havana_transcript_version "1"; tag "basic";
chr22   havana  exon    43367775    43367832    .   +   .   gene_id "ENSG00000100403"; gene_version "10"; transcript_id "ENST00000486331"; transcript_version "1"; exon_number "1"; gene_name "ZC3H7B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ZC3H7B-002"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000320697"; havana_transcript_version "1"; exon_id "ENSE00001942555"; exon_version "1";