VcfScanUpstreamOrf

Last commit

Scan BAM for upstream-ORF. Inspired from https://github.com/ImperialCardioGenetics/uORFs

Usage

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

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

Usage: vcfscanupstreamorf [options] Files
  Options:
    --archive
      Export an archive containing the fasta+bed of the uORF is created and 
      the program exits. An existing directory or a filename ending with the 
      '.zip' or '.tar' or '.tar.gz' suffix.
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    --canonical
      reduce the number of transcripts. Keep one if some share the same UTR
      Default: false
    --dac
      disable scan for ATG creation
      Default: false
    --dad
      disable scan for ATG deletion
      Default: false
    --dsc
      disable scan for STOP creation
      Default: false
    --dsd
      disable scan for STOP deletion
      Default: false
    --exclude-cds
      remove a uORF it if enterely overlaps a coding region of the exon of an 
      alternative transcript.
      Default: false
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
  * -gtf, --gtf
      A GTF (General Transfer Format) file. See 
      https://www.ensembl.org/info/website/upload/gff.html . Please note that 
      CDS are only detected if a start and stop codons are defined.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --kal
      disable scan for Kozak change
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
  * -r, -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --strong
      only accept events that are related to 'Strong' Kozak pattern.
      Default: false
    --uorf-only
      only print variants having something to say about an uorf
      Default: false
    --version
      print version and exit

Keywords

vcf
uorf

Creation Date

20190218

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/upstreamorf/VcfScanUpstreamOrf.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/upstreamorf/VcfScanUpstreamOrfTest.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 vcfscanupstreamorf ? 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

inspiration

part of this code was inspired from: https://github.com/ImperialCardioGenetics/uORFs/blob/master/5primeUTRannotator/five_prime_UTR_annotator.pm

Examples

Example 1

 wget -q -O - "https://storage.googleapis.com/gnomad-public/release/2.1/vcf/genomes/gnomad.genomes.r2.1.sites.chr1.vcf.bgz" |\
 bcftools annotate -x "INFO,FILTER" |\
 java -jar /home/lindenb/src/jvarkit-git/dist/vcfscanupstreamorf.jar \
    -R human_g1k_v37.fasta  --uorf-only  --canonical  

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   89333   rs1008713359    A   G   283.15  .   UORF_DEL_ATG=transcript:ENST00000466430.1|strand:-|utr-start:89295|utr-end:120932|alt:C|atg-pos:89334|cap-atg:2708|atg-cds:40|atg-frame:atg-out-of-cds-frame|kozak-seq:GAAATGC|kozak-strength:Moderate|stop-frame:not-in-frame-stop|stop-pos:89318|atg-stop:16|pep:.
1   89359   rs1327179626    C   T   3839.47 .   UORF_ADD_ATG=transcript:ENST00000466430.1|strand:-|utr-start:89295|utr-end:120932|alt:A|atg-pos:89359|cap-atg:2683|atg-cds:65|atg-frame:atg-out-of-cds-frame|kozak-seq:TGCATGT|kozak-strength:Weak|stop-frame:in-frame-stop|stop-pos:89356|atg-stop:3|pep:M
1   89391   rs1332733110    T   C   2045.80 .   UORF_DEL_ATG=transcript:ENST00000466430.1|strand:-|utr-start:89295|utr-end:120932|alt:G|atg-pos:89391|cap-atg:2651|atg-cds:97|atg-frame:atg-out-of-cds-frame|kozak-seq:TGAATGA|kozak-strength:Weak|stop-frame:in-frame-stop|stop-pos:89382|atg-stop:9|pep:VNK
1   89555   rs1200434471    A   C   283.62  .   UORF_ADD_ATG=transcript:ENST00000466430.1|strand:-|utr-start:89295|utr-end:120932|alt:G|atg-pos:89557|cap-atg:2485|atg-cds:263|atg-frame:atg-out-of-cds-frame|kozak-seq:GAAATGA|kozak-strength:Moderate|stop-frame:in-frame-stop|stop-pos:89452|atg-stop:105|pep:MKSQNVSQKIIYNVCVRKRQYPSNFESLHQKENSK,transcript:ENST00000495576.1|strand:-|utr-start:89551|utr-end:91105|alt:G|atg-pos:89557|cap-atg:1312|atg-cds:7|atg-frame:atg-out-of-cds-frame|kozak-seq:GAAATGA|kozak-strength:Moderate|stop-frame:not-in-frame-stop|stop-pos:89556|atg-stop:1|pep:.
1   89560   rs1234719556    C   A   448.62  .   UORF_DEL_ATG=transcript:ENST00000466430.1|strand:-|utr-start:89295|utr-end:120932|alt:T|atg-pos:89562|cap-atg:2480|atg-cds:268|atg-frame:atg-out-of-cds-frame|kozak-seq:TGAATGA|kozak-strength:Weak|stop-frame:in-frame-stop|stop-pos:89541|atg-stop:21|pep:IKLKVKM,transcript:ENST00000495576.1|strand:-|utr-start:89551|utr-end:91105|alt:T|atg-pos:89562|cap-atg:1307|atg-cds:12|atg-frame:atg-in-cds-frame|kozak-seq:TGAATGA|kozak-strength:Weak|stop-frame:not-in-frame-stop|stop-pos:89555|atg-stop:7|pep:.
1   89624   rs1166058274    T   C   606.05  .   UORF_DEL_ATG=transcript:ENST00000466430.1|strand:-|utr-start:89295|utr-end:120932|alt:G|atg-pos:89624|cap-atg:2418|atg-cds:330|atg-frame:atg-in-cds-frame|kozak-seq:ACAATGA|kozak-strength:Moderate|stop-frame:in-frame-stop|stop-pos:89609|atg-stop:15|pep:VKELF,transcript:ENST00000495576.1|strand:-|utr-start:89551|utr-end:91105|alt:G|atg-pos:89624|cap-atg:1245|atg-cds:74|atg-frame:atg-out-of-cds-frame|kozak-seq:ACAATGA|kozak-strength:Moderate|stop-frame:in-frame-stop|stop-pos:89609|atg-stop:15|pep:VKELF
1   89718   rs865856422 A   G   1466.11 .   UORF_DEL_ATG=transcript:ENST00000466430.1|strand:-|utr-start:89295|utr-end:120932|alt:C|atg-pos:89719|cap-atg:2323|atg-cds:425|atg-frame:atg-out-of-cds-frame|kozak-seq:AAAATGA|kozak-strength:Moderate|stop-frame:in-frame-stop|stop-pos:89710|atg-stop:9|pep:TKL,transcript:ENST00000495576.1|strand:-|utr-start:89551|utr-end:91105|alt:C|atg-pos:89719|cap-atg:1150|atg-cds:169|atg-frame:atg-out-of-cds-frame|kozak-seq:AAAATGA|kozak-strength:Moderate|stop-frame:in-frame-stop|stop-pos:89710|atg-stop:9|pep:TKL
1   89831   rs1209426147    A   G   372.62  .   UORF_DEL_ATG=transcript:ENST00000466430.1|strand:-|utr-start:89295|utr-end:120932|alt:C|atg-pos:89832|cap-atg:2210|atg-cds:538|atg-frame:atg-out-of-cds-frame|kozak-seq:CTTATGT|kozak-strength:Weak|stop-frame:in-frame-stop|stop-pos:89811|atg-stop:21|pep:TFAIYHT,transcript:ENST00000495576.1|strand:-|utr-start:89551|utr-end:91105|alt:C|atg-pos:89832|cap-atg:1037|atg-cds:282|atg-frame:atg-in-cds-frame|kozak-seq:CTTATGT|kozak-strength:Weak|stop-frame:in-frame-stop|stop-pos:89811|atg-stop:21|pep:TFAIYHT
1   89945   rs1376722481    G   C   297.51  .   UORF_ADD_ATG=transcript:ENST00000466430.1|strand:-|utr-start:89295|utr-end:120932|alt:G|atg-pos:89947|cap-atg:2095|atg-cds:653|atg-frame:atg-out-of-cds-frame|kozak-seq:AATATGC|kozak-strength:Moderate|stop-frame:in-frame-stop|stop-pos:89803|atg-stop:144|pep:MPLASVSHLAKPRLRSGKMEAISSWERRQRRWEYYVATYVCNLPYLAL,transcript:ENST00000495576.1|strand:-|utr-start:89551|utr-end:91105|alt:G|atg-pos:89947|cap-atg:922|atg-cds:397|atg-frame:atg-out-of-cds-frame|kozak-seq:AATATGC|kozak-strength:Moderate|stop-frame:in-frame-stop|stop-pos:89803|atg-stop:144|pep:MPLASVSHLAKPRLRSGKMEAISSWERRQRRWEYYVATYVCNLPYLAL
1   90032   rs866094671 C   T   14378.50    .   UORF_ADD_ATG=transcript:ENST00000466430.1|strand:-|utr-start:89295|utr-end:120932|alt:A|atg-pos:90032|cap-atg:2010|atg-cds:738|atg-frame:atg-in-cds-frame|kozak-seq:TTCATGG|kozak-strength:Moderate|stop-frame:in-frame-stop|stop-pos:89951|atg-stop:81|pep:MGQLVSRAARETKPQCTFYSLCAHQTC,transcript:ENST00000495576.1|strand:-|utr-start:89551|utr-end:91105|alt:A|atg-pos:90032|cap-atg:837|atg-cds:482|atg-frame:atg-out-of-cds-frame|kozak-seq:TTCATGG|kozak-strength:Moderate|stop-frame:in-frame-stop|stop-pos:89951|atg-stop:81|pep:MGQLVSRAARETKPQCTFYSLCAHQTC

extract to bed format

track name="uORF" description="uORF for http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz"
#chrom  chromStart  chromEnd    name    score   strand  thickStart  thickEnd    itemRgb blockCount  blockSizes  blockStarts
chr1    34553   36081   ENST00000417324.1.uorf  100 -   35140   35736   0,0,255 1   1528    0
chr1    89294   120932  ENST00000466430.1.uorf  500 -   91254   91491   0,255,0 1   31638   0
chr1    89550   91105   ENST00000495576.1.uorf  100 -   90431   90590   0,0,255 1   1555    0
chr1    139789  140339  ENST00000493797.1.uorf  500 -   139816  140223  0,255,0 1   550 0
chr1    141473  149707  ENST00000484859.1.uorf  1000    -   146708  146978  255,0,0 1   8234    0
chr1    142807  146831  ENST00000490997.1.uorf  1000    -   142988  146482  255,0,0 1   4024    0
chr1    157783  157887  ENST00000410691.1.uorf  0   -   157848  157887  0,0,0   1   104 0
chr1    236111  267253  ENST00000424587.2.uorf  100 -   236759  236918  0,0,255 1   31142   0
chr1    453632  460480  ENST00000450983.1.uorf  1000    -   453980  454166  255,0,0 1   6848    0
chr1    521368  523833  ENST00000417636.1.uorf  500 -   522285  523620  0,255,0 1   2465    0
chr1    529838  532878  ENST00000357876.5.uorf  500 -   530001  532684  0,255,0 1   3040    0
chr1    562756  564390  ENST00000452176.1.uorf  500 -   562878  562995  0,255,0 1   1634    0
chr1    646721  655580  ENST00000414688.1.uorf  500 -   647189  655553  0,255,0 1   8859    0
chr1    677192  685396  ENST00000416385.1.uorf  100 -   682910  683180  0,0,255 1   8204    0
chr1    693612  693716  ENST00000411249.1.uorf  0   -   693689  693716  0,0,0   1   104 0
chr1    694411  700305  ENST00000417659.1.uorf  100 -   700133  700208  0,0,255 1   5894    0
chr1    700236  714006  ENST00000428504.1.uorf  500 -   705034  709660  0,255,0 1   13770   0
chr1    736258  745541  ENST00000447500.1.uorf  500 -   741231  745515  0,255,0 1   9283    0
chr1    745488  753092  ENST00000435300.1.uorf  500 -   752900  753047  0,255,0 1   7604    0
chr1    761585  762902  ENST00000473798.1.uorf  500 -   762082  762571  0,255,0 1   1317    0
chr1    803450  812283  ENST00000446136.1.uorf  100 -   810390  812268  0,0,255 1   8833    0
chr1    852249  855072  ENST00000417705.1.uorf  100 -   852976  854794  0,0,255 1   2823    0
chr1    889805  894689  ENST00000487214.1.uorf  1000    -   889839  894620  255,0,0 1   4884    0
chr1    916546  917473  ENST00000341290.2.uorf  1000    -   916549  917473  255,0,0 1   927 0
chr1    931345  933431  ENST00000606034.1.uorf  100 -   931510  932137  0,0,255 1   2086    0
chr1    935353  935552  ENST00000428771.2.uorf  500 -   935487  935544  0,255,0 1   199 0
chr1    947376  948573  ENST00000458555.1.uorf  100 -   947459  947507  0,0,255 1   1197    0
chr1    997587  998668  ENST00000442292.2.uorf  500 -   997810  998119  0,255,0 1   1081    0
chr1    1019305 1051623 ENST00000482816.1.uorf  1000    -   1019401 1026923 255,0,0 1   32318   0
chr1    1026923 1027554 ENST00000379320.1.uorf  100 -   1027028 1027400 0,0,255 1   631 0
chr1    1026923 1041507 ENST00000379319.1.uorf  100 -   1041338 1041410 0,0,255 1   14584   0
(...)