jvarkit

VcfFilterSequenceOntology

Last commit

Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology. Reasoning : Children of user’s SO-terms will be also used.

Usage

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

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

Usage: vcffilterso [options] Files
  Options:
    -A, --acn, --accession
      add this SO:ACN. e.g.: 'SO:0001818' Protein altering variant [http://www.sequenceontology.org/miso/current_svn/term/SO:0001818](http://www.sequenceontology.org/miso/current_svn/term/SO:0001818)
      Default: []
    -f, --acnfile
      file of SO accession numbers, one per line
    --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
    --disable-vc-attribute-recalc
      When genotypes are removed/changed, Dd not recalculate variant 
      attributes like DP, AF, AC, AN...
      Default: false
    -fi, --filterin
      Do not discard variant but add this FILTER its' prediction is found in 
      the database
    -fo, --filterout
      Do not discard variant but add this FILTER its' prediction is NOT found 
      in the database
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -i, --invert
      invert SO:Term selection
      Default: false
    -d, --noreasoning
      disable reasoning: do not use SO term's children.
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    -owluri, --owluri
      Experimental. If not empty, don't use the internal SO ontology but load 
      a OWL description of the ontology. Tested with https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/releases/so-xp.owl/so-xp-simple.owl
      Default: <empty string>
    -r, --rmatt, --remove-attribute
      Do not remove the variant itself, just remove the mismatching Prediction 
      in the INFO column: e.g: CSQ=OK,OK,NO,OK -> CSQ=OK,OK,OK.
      Default: false
    -R, --rmnoatt, --remove-variant-if-no-INFO
      remove the variant if option -r was used and the is no more attribute
      Default: false
    -S, --showacn
      list the available SO terms and exit.
      Default: false
    --vc-attribute-recalc-ignore-filtered
      When recalculating variant attributes like DP AF, AC, AN, ignore 
      FILTERed **Genotypes**
      Default: false
    --vc-attribute-recalc-ignore-missing
      Ignore missing VCF headers (DP, AF, AC, AN). Default behavior: adding 
      VCF header if they're missing
      Default: false
    --version
      print version and exit

Keywords

See also in Biostars

Creation Date

20170331

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterso/VcfFilterSequenceOntology.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcffilterso/VcfFilterSequenceOntologyTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcffilterso ? 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

Examples

Example

list the variants having a “feature_elongation” ( SO:0001907 ) http://www.sequenceontology.org/browser/current_release/term/SO:0001907

here the variant is selected because stop_lost is a children of SO:0001907 .

$ curl -s -k "https://raw.github.com/arq5x/gemini/master/test/test5.vep.snpeff.vcf" | \
java -jar dist/vcffilterso.jar  -A "SO:0001907"  |\
grep -v "##"

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	M10475	M10478	M10500M128215
chr10	1142208	.	T	C	3404.30	.	AC=8;AF=1.00;AN=8;CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150|||,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154|||,intron_variant|||ENSG00000047056|WDR37|ENST00000358220|||,stop_lost|Tga/Cga|* / R|ENSG00000047056|WDR37|ENST00000381329|9/9||;DP=122;Dels=0.00;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|9),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|9),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|);FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90	GT:AD:DP:GQ:PL	1/1:1,37:39:87.16:940,87,0	1/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0	1/1:0,30:30:75.18:836,75,0

Example

invert the query:

$ curl -s -k "https://raw.github.com/arq5x/gemini/master/test/test5.vep.snpeff.vcf" | \
java -jar dist/vcffilterso.jar -v -A "SO:0001907"  |\
grep -v "##"

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	M10475	M10478	M10500M128215
chr1	145273345	.	T	C	289.85	.	AC=3;AF=0.38;AN=8;BaseQRankSum=1.062;CSQ=missense_variant|Tct/Cct|S/P|ENSG00000213240|NOTCH2NL|ENST00000369340|4/6|benign(0.238)|tolerated(0.45),missense_variant|Tct/Cct|S/P|ENSG00000213240|NOTCH2NL|ENST00000362074|3/5|benign(0.238)|tolerated(0.45),missense_variant&amp;NMD_transcript_variant|Tct/Cct|S/P|ENSG00000255168||ENST00000468030|3/23|benign(0.416)|tolerated(0.55),missense_variant|Tct/Cct|S/P|ENSG00000213240|NOTCH2NL|ENST00000344859|3/6|possibly_damaging(0.545)|tolerated(0.44);DP=1000;DS;Dels=0.00;EFF=EXON(MODIFIER|||||RP11-458D21.5|nonsense_mediated_decay|NON_CODING|ENST00000468030|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S67P|230|NOTCH2NL|protein_coding|CODING|ENST00000344859|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S67P|236|NOTCH2NL|protein_coding|CODING|ENST00000362074|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S67P|236|NOTCH2NL|protein_coding|CODING|ENST00000369340|);FS=3.974;HRun=1;HaplotypeScore=17.4275;MQ=29.25;MQ0=0;MQRankSum=-1.370;QD=0.39;ReadPosRankSum=-1.117	GT:AD:DP:GQ:PL	0/0:226,22:250:99:0,158,4259	0/1:224,24:250:5.77:6,0,5314	0/1:219,28:249:57.30:57,0,5027	0/1:215,34:250:99:269,0,3796
chr1	156011444	.	T	C	2523.46	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.490;CSQ=missense_variant|atA/atG|I/M|ENSG00000160803|UBQLN4|ENST00000368309|10/11|benign(0.012)|tolerated(0.3),downstream_gene_variant|||ENSG00000160803|UBQLN4|ENST00000459954|||,missense_variant|Atc/Gtc|I/V|ENSG00000160803|UBQLN4|ENST00000368307|6/7|unknown(0)|tolerated(0.88);DP=204;Dels=0.00;EFF=DOWNSTREAM(MODIFIER|||||UBQLN4|processed_transcript|CODING|ENST00000459954|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I148V|226|UBQLN4|protein_coding|CODING|ENST00000368307|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I495M|601|UBQLN4|protein_coding|CODING|ENST00000368309|);FS=4.328;HRun=0;HaplotypeScore=4.3777;MQ=35.24;MQ0=0;MQRankSum=-0.101;QD=14.93;ReadPosRankSum=1.575	GT:AD:DP:GQ:PL	0/1:24,15:40:99:214,0,443	0/1:32,36:68:99:702,0,794	1/1:1,59:61:99:1656,132,0	0/0:34,1:35:69.10:0,69,717
chr5	64982321	.	T	C	61.12	.	AC=4;AF=1.00;AN=4;CSQ=intron_variant|||ENSG00000197860|SGTB|ENST00000381007|||,intron_variant|||ENSG00000197860|SGTB|ENST00000506816|||;DP=4;Dels=0.00;EFF=INTRON(MODIFIER||||194|SGTB|protein_coding|CODING|ENST00000506816|5),INTRON(MODIFIER||||304|SGTB|protein_coding|CODING|ENST00000381007|5);FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=20.37	GT:AD:DP:GQ:PL	1/1:0,2:2:6:58,6,0	1/1:0,1:1:3.01:37,3,0	./.	./.
chr10	126678092	.	G	A	89.08	.	AC=1;AF=0.13;AN=8;BaseQRankSum=-3.120;CSQ=stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000531469|11/11||,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000309035|9/9||,downstream_gene_variant|||ENSG00000019995|ZRANB1|ENST00000359653|||,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000494626|11/11||,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000337195|11/11||,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000334808|9/9||,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000411419|11/11||,downstream_gene_variant|||ENSG00000175029|CTBP2|ENST00000395705|||;DP=185;Dels=0.00;EFF=DOWNSTREAM(MODIFIER||||708|ZRANB1|protein_coding|CODING|ENST00000359653|),DOWNSTREAM(MODIFIER|||||CTBP2|processed_transcript|CODING|ENST00000395705|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000337195|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000411419|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000494626|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000531469|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q513*|513|CTBP2|protein_coding|CODING|ENST00000334808|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q985*|985|CTBP2|protein_coding|CODING|ENST00000309035|);FS=3.490;HRun=0;HaplotypeScore=3.3843;MQ=25.32;MQ0=0;MQRankSum=6.568;QD=2.02;ReadPosRankSum=-5.871	GT:AD:DP:GQ:PL	0/0:64,3:67:99:0,165,1505	0/0:11,1:12:7.31:0,7,240	0/0:52,10:62:54.97:0,55,1263	0/1:35,9:44:99:125,0,693
chr10	135210791	.	T	C	65.41	.	AC=4;AF=0.50;AN=8;BaseQRankSum=2.054;CSQ=intron_variant|||ENSG00000148824||ENST00000317502|||,upstream_gene_variant|||ENSG00000148824||ENST00000492266|||,intron_variant&amp;nc_transcript_variant|||ENSG00000148824||ENST00000460848|||,intron_variant|||ENSG00000254536|MTG1|ENST00000468317|||,intron_variant&amp;nc_transcript_variant|||ENSG00000148824||ENST00000477902|||,intron_&amp;nc_transcript_variant|||ENSG00000148824||ENST00000473735|||,intron_variant&amp;nc_transcript_variant|||ENSG00000148824||ENST00000498790|||,intron_variant|||ENSG00000148824||ENST00000432508|||,intron_variant&amp;nc_transcript_variant|||ENSG00000148824||ENST00000498334|||,intron_variant&amp;nc_transcript_variant|||ENSG00000148824||ENST00000495014|||;DP=11;Dels=0.00;EFF=INTRON(MODIFIER||||283|MTG1|protein_coding|CODING|ENST00000432508|3),INTRON(MODIFIER||||334|MTG1|protein_coding|CODING|ENST00000317502|3),INTRON(MODIFIER||||339|MTG1|protein_coding|CODING|ENST00000468317|4),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000460848|3),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000473735|3),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000477902|3),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000495014|3),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000498334|3),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000498790|3),UPSTREAM(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000492266|);FS=0.000;HRun=0;HaplotypeScore=0.2489;MQ=35.12;MQ0=0;MQRankSum=0.248;QD=16.35;ReadPosRankSum=-1.001	GT:AD:DP:GQ:PL	0/0:4,0:4:9:0,9,84	1/1:0,3:3:6.02:74,6,0	1/1:0,1:1:3.01:37,3,0	0/0:3,0:3:9.02:0,9,100
chr13	48873835	.	G	A	58.95	.	AC=4;AF=1.00;AN=4;CSQ=upstream_gene_variant|||ENSG00000139687|RB1|ENST00000467505|||,upstream_gene_variant|||ENSG00000139687|RB1|ENST00000525036|||,downstream_gene_variant|||ENSG00000231473|LINC00441|ENST00000436963|||,upstream_gene_variant|||ENSG00000139687|RB1|ENST00000267163|||,intron_variant&amp;nc_transcript_variant|||ENSG00000231473|LINC00441|ENST00000433480|||;DP=3;Dels=0.00;EFF=DOWNSTREAM(MODIFIER|||||LINC00441|processed_transcript|NON_CODING|ENST00000436963|),INTRON(MODIFIER|||||LINC00441|processed_transcript|NON_CODING|ENST00000433480|2),UPSTREAM(MODIFIER||||928|RB1|protein_coding|CODING|ENST00000267163|),UPSTREAM(MODIFIER|||||RB1|nonsense_mediated_decay|CODING|ENST00000467505|),UPSTREAM(MODIFIER|||||RB1|retained_intron|CODING|ENST00000525036|);FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=19.65	GT:AD:DP:GQ:PL	./.	./.	1/1:0,2:2:6.01:62,6,0	1/1:0,1:1:3.01:31,3,0
chr20	36779424	.	G	A	128.76	.	AC=1;AF=0.13;AN=8;BaseQRankSum=0.610;CSQ=non_coding_exon_variant&amp;nc_transcript_variant|||ENSG00000198959|TGM2|ENST00000468262|4/10||,non_coding_exon_variant&amp;nc_transcript_variant|||ENSG00000198959|TGM2|ENST00000485572|4/13||,non_coding_exon_variant&amp;nc_transcript_variant|||ENSG00000198959|TGM2|ENST00000474777|4/6||,stop_gained|Cag/Tag|Q/*|ENSG00000198959|TGM2|ENST00000373403|5/7||,stop_gained|Cag/Tag|Q/*|ENSG00000198959|TGM2|ENST00000361475|4/13||,stop_gained|Cag/Tag|Q/*|ENSG00000198959|TGM2|ENST00000453095|5/5||,stop_gained|Cag/Tag|Q/*|ENSG00000198959|TGM2|ENST00000536701|3/12||,stop_gained|Cag/Tag|Q/*|ENSG00000198959|TGM2|ENST00000536724|3/12||;DP=196;Dels=0.00;EFF=EXON(MODIFIER|||||TGM2|processed_transcript|CODING|ENST00000485572|4),EXON(MODIFIER|||||TGM2|retained_intron|CODING|ENST00000468262|4),EXON(MODIFIER|||||TGM2|retained_intron|CODING|ENST00000474777|4),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q157*|158|TGM2|protein_coding|CODING|ENST00000453095|),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q157*|279|TGM2|protein_coding|CODING|ENST00000373403|),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q157*|687|TGM2|protein_coding|CODING|ENST00000361475|),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q76*|606|TGM2|protein_coding|CODING|ENST00000536701|),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q97*|627|TGM2|protein_coding|CODING|ENST00000536724|);FS=1.447;HRun=0;HaplotypeScore=4.5749;MQ=36.22;MQ0=0;MQRankSum=-0.814;QD=3.90;ReadPosRankSum=-0.570	GT:AD:DP:GQ:PL	0/0:49,1:52:63.68:0,64,969	0/0:17,0:17:30.05:0,30,320	0/0:93,0:94:99:0,216,2384	0/1:24,9:33:99:165,0,505
chrX	17819377	.	T	C	7515.25	.	AC=8;AF=1.00;AN=8;CSQ=downstream_gene_variant|||ENSG00000248906||ENST00000509491|||,missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000360011|3/3|unknown(0)|tolerated(1),missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000331511|3/3|unknown(0)|tolerated(1),missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000415486|3/3|unknown(0)|tolerated(1),missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000451717|2/2|unknown(0)|tolerated(1),missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000545871|3/3|unknown(0)|tolerated(1);DP=319;Dels=0.00;EFF=DOWNSTREAM(MODIFIER|||||RP3-389A20.4|processed_transcript|NON_CODING|ENST00000509491|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M202V|480|RAI2|protein_coding|CODING|ENST00000415486|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M252V|530|RAI2|protein_coding|CODING|ENST00000331511|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M252V|530|RAI2|protein_coding|CODING|ENST00000360011|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M252V|530|RAI2|protein_coding|CODING|ENST00000451717|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M252V|530|RAI2|protein_coding|CODING|ENST00000545871|);FS=0.000;HRun=1;HaplotypeScore=7.7850;MQ=36.33;MQ0=0;QD=23.56	GT:AD:DP:GQ:PL	1/1:0,125:126:99:2343,237,0	1/1:0,26:26:78.14:837,78,0	1/1:0,90:92:99:2640,244,0	1/1:0,74:75:99:1695,171,0

Example

list the available SO:terms:

$  java -jar dist/vcffilterso.jar -S

SO:0001650	inframe_variant
SO:0001791	exon_variant
SO:0001792	non_coding_exon_variant
SO:0001593	minus_2_frameshift_variant
SO:0001594	plus_1_frameshift_variant
SO:0001595	plus_2_frameshift_variant
SO:0001596	transcript_secondary_structure_variant
SO:0001597	compensatory_transcript_secondary_structure_variant
SO:0001598	translational_product_structure_variant
SO:0001599	3D_polypeptide_structure_variant
(...)

See also

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