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Commit c7717d8c authored by Pradat Yoann's avatar Pradat Yoann
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remove gitlab ci; add badges

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.gitlab-ci.yml deleted 100644 → 0
View file @ b4784d84
image: "python:3.9"
default:
tags:
- docker
stages:
- test
variables:
CODECOV_TOKEN: "c8bcf054-f0cb-4bf1-8866-1b862905ef89"
before_script:
- make install
test:
stage: test
script:
- make test
- bash <(curl -s https://codecov.io/bash)
only:
refs:
- master
Makefile
View file @ c7717d8c
......@@ -24,6 +24,9 @@ test:
$(PIP) install --upgrade pytest pytest-cov
$(PYTEST) --cov-config=.coveragerc --cov-report term-missing --cov . .
codecov:
bash <(curl -s https://codecov.io/bash) -t c8bcf054-f0cb-4bf1-8866-1b862905ef89
build:
@echo "---------------Build variant_annotator-----------------"
$(PYTHON) -m pip install --user --upgrade setuptools wheel
......
README.md
View file @ c7717d8c
# Biotool for annotating variants from a VCF file.
[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
[![codecov](https://codecov.io/gh/ypradat/VariantAnnotator/branch/master/graph/badge.svg?token=H821S3WZHS)](https://codecov.io/gh/ypradat/VariantAnnotator)
The tool is divided in 3 steps
- Manual parsing of the VCF
- Run [vcf2maf](https://github.com/mskcc/vcf2maf) to extract standard information
......@@ -7,7 +10,7 @@ The tool is divided in 3 steps
## 1. What is the tool doing ?
VEP annotates variants with information from multiple external databases and can be configure for to answer a lot of
VEP annotates variants with information from multiple external databases and can be configured to answer a lot of
specific needs. For more details, see [VEP's options
page](https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html). VEP does not however extract information
like number of reads or somatic status from the VCF file. vcf2maf is supposed to perform these tasks but failed to do on
......
coverage.xml 0 → 100644
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examples/results_old/TCGA_GA/maf/TCGA-A1-A0SB_db9d40fb-bfce-4c3b-a6c2-41c5c88982f1_a3254f8e-3bbd-42fc-abea-a5f25b7648b3.indel.capture.tcga.txt 0 → 100644
View file @ c7717d8c
n_GT n_SS n_TIR n_TAR n_DP n_DP4 n_AD n_depth n_ref_count n_alt_count t_GT t_SS t_TIR t_TAR t_DP t_DP4 t_AD t_depth t_ref_count t_alt_count Variant_Quality Filter_VCF Hugo_Symbol_VCF2MAF Entrez_Gene_Id_VCF2MAF Center_VCF2MAF NCBI_Build_VCF2MAF Chromosome_VCF2MAF Start_Position_VCF2MAF End_Position_VCF2MAF Strand_VCF2MAF Variant_Classification_VCF2MAF Variant_Type_VCF2MAF Reference_Allele_VCF2MAF Tumor_Seq_Allele1_VCF2MAF Tumor_Seq_Allele2_VCF2MAF dbSNP_RS_VCF2MAF dbSNP_Val_Status_VCF2MAF Tumor_Sample_Barcode_VCF2MAF Matched_Norm_Sample_Barcode_VCF2MAF Match_Norm_Seq_Allele1_VCF2MAF Match_Norm_Seq_Allele2_VCF2MAF Tumor_Validation_Allele1_VCF2MAF Tumor_Validation_Allele2_VCF2MAF Match_Norm_Validation_Allele1_VCF2MAF Match_Norm_Validation_Allele2_VCF2MAF Verification_Status_VCF2MAF Validation_Status_VCF2MAF Mutation_Status_VCF2MAF Sequencing_Phase_VCF2MAF Sequence_Source_VCF2MAF Validation_Method_VCF2MAF Score_VCF2MAF BAM_File_VCF2MAF Sequencer_VCF2MAF Tumor_Sample_UUID_VCF2MAF Matched_Norm_Sample_UUID_VCF2MAF HGVSc_VCF2MAF HGVSp_VCF2MAF HGVSp_Short_VCF2MAF Transcript_ID_VCF2MAF Exon_Number_VCF2MAF t_depth_VCF2MAF t_ref_count_VCF2MAF t_alt_count_VCF2MAF n_depth_VCF2MAF n_ref_count_VCF2MAF n_alt_count_VCF2MAF all_effects_VCF2MAF Allele_VCF2MAF Gene_VCF2MAF Feature_VCF2MAF Feature_type_VCF2MAF Consequence_VCF2MAF cDNA_position_VCF2MAF CDS_position_VCF2MAF Protein_position_VCF2MAF Amino_acids_VCF2MAF Codons_VCF2MAF Existing_variation_VCF2MAF ALLELE_NUM_VCF2MAF DISTANCE_VCF2MAF STRAND_VEP_VCF2MAF SYMBOL_VCF2MAF SYMBOL_SOURCE_VCF2MAF HGNC_ID_VCF2MAF BIOTYPE_VCF2MAF CANONICAL_VCF2MAF CCDS_VCF2MAF ENSP_VCF2MAF SWISSPROT_VCF2MAF TREMBL_VCF2MAF UNIPARC_VCF2MAF RefSeq_VCF2MAF SIFT_VCF2MAF PolyPhen_VCF2MAF EXON_VCF2MAF INTRON_VCF2MAF DOMAINS_VCF2MAF AF_VCF2MAF AFR_AF_VCF2MAF AMR_AF_VCF2MAF ASN_AF_VCF2MAF EAS_AF_VCF2MAF EUR_AF_VCF2MAF SAS_AF_VCF2MAF AA_AF_VCF2MAF EA_AF_VCF2MAF CLIN_SIG_VCF2MAF SOMATIC_VCF2MAF PUBMED_VCF2MAF MOTIF_NAME_VCF2MAF MOTIF_POS_VCF2MAF HIGH_INF_POS_VCF2MAF MOTIF_SCORE_CHANGE_VCF2MAF IMPACT_VCF2MAF PICK_VCF2MAF VARIANT_CLASS_VCF2MAF TSL_VCF2MAF HGVS_OFFSET_VCF2MAF PHENO_VCF2MAF MINIMISED_VCF2MAF ExAC_AF_VCF2MAF ExAC_AF_AFR_VCF2MAF ExAC_AF_AMR_VCF2MAF ExAC_AF_EAS_VCF2MAF ExAC_AF_FIN_VCF2MAF ExAC_AF_NFE_VCF2MAF ExAC_AF_OTH_VCF2MAF ExAC_AF_SAS_VCF2MAF GENE_PHENO_VCF2MAF FILTER_VCF2MAF flanking_bps_VCF2MAF vcf_id_VCF2MAF vcf_qual_VCF2MAF ExAC_AF_Adj_VCF2MAF ExAC_AC_AN_Adj_VCF2MAF ExAC_AC_AN_VCF2MAF ExAC_AC_AN_AFR_VCF2MAF ExAC_AC_AN_AMR_VCF2MAF ExAC_AC_AN_EAS_VCF2MAF ExAC_AC_AN_FIN_VCF2MAF ExAC_AC_AN_NFE_VCF2MAF ExAC_AC_AN_OTH_VCF2MAF ExAC_AC_AN_SAS_VCF2MAF ExAC_FILTER_VCF2MAF gnomAD_AF_VCF2MAF gnomAD_AFR_AF_VCF2MAF gnomAD_AMR_AF_VCF2MAF gnomAD_ASJ_AF_VCF2MAF gnomAD_EAS_AF_VCF2MAF gnomAD_FIN_AF_VCF2MAF gnomAD_NFE_AF_VCF2MAF gnomAD_OTH_AF_VCF2MAF gnomAD_SAS_AF_VCF2MAF vcf_pos_VCF2MAF #Uploaded_variation_VEP Location_VEP Allele_VEP Gene_VEP Feature_VEP Feature_type_VEP Consequence_VEP cDNA_position_VEP CDS_position_VEP Protein_position_VEP Amino_acids_VEP Codons_VEP Existing_variation_VEP Extra_VEP IMPACT_VEP STRAND_VEP SYMBOL_VEP SYMBOL_SOURCE_VEP HGNC_ID_VEP BIOTYPE_VEP CANONICAL_VEP CCDS_VEP ENSP_VEP SWISSPROT_VEP UNIPARC_VEP INTRON_VEP HGVSc_VEP AFR_AF_VEP AMR_AF_VEP EAS_AF_VEP EUR_AF_VEP SAS_AF_VEP MAX_AF_VEP MAX_AF_POPS_VEP TREMBL_VEP EXON_VEP HGVSp_VEP gnomAD_AF_VEP gnomAD_AFR_AF_VEP gnomAD_AMR_AF_VEP gnomAD_ASJ_AF_VEP gnomAD_EAS_AF_VEP gnomAD_FIN_AF_VEP gnomAD_NFE_AF_VEP gnomAD_OTH_AF_VEP gnomAD_SAS_AF_VEP HGVS_OFFSET_VEP Tumor_Sample Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Tumor_Sample_Site
0/0 2 11 11,0 11.0 11.0 0.0 0/1 2 6 4,2 6.0 50 PASS FAM131C 348487 . GRCh37 1 16386305 16386306 + Intron INS - - C rs372070031 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 - - c.451+58dup ENST00000375662 FAM131C,intron_variant,,ENST00000375662,NM_182623.2;CLCNKB,downstream_gene_variant,,ENST00000375667,NM_001165945.2;CLCNKB,downstream_gene_variant,,ENST00000375679,NM_000085.4;CLCNKB,downstream_gene_variant,,ENST00000431772,;FAM131C,intron_variant,,ENST00000494078,; C ENSG00000185519 ENST00000375662 Transcript intron_variant rs372070031 1 -1 FAM131C HGNC 26717 protein_coding YES CCDS41270.1 ENSP00000364814 Q96AQ9 UPI000022B016 NM_182623.2 5/6 0.2731 0.3573 0.3581 0.3757 0.5051 MODIFIER 1 insertion PASS GGC rs143272992 50 16386305 rs143272992 1:16386305-16386306 C ENSG00000185519 ENST00000375662.4 Transcript intron_variant - - - - - rs372070031 IMPACT=MODIFIER;STRAND=-1;SYMBOL=FAM131C;SYMBOL_SOURCE=HGNC;HGNC_ID=26717;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS41270.1;ENSP=ENSP00000364814;SWISSPROT=Q96AQ9;UNIPARC=UPI000022B016;INTRON=5/6;HGVSc=ENST00000375662.4:c.451+58dup;AFR_AF=0.2731;AMR_AF=0.3573;EAS_AF=0.3581;EUR_AF=0.3757;SAS_AF=0.5051;MAX_AF=0.5051;MAX_AF_POPS=SAS MODIFIER -1 FAM131C HGNC 26717 protein_coding YES CCDS41270.1 ENSP00000364814 Q96AQ9 UPI000022B016 5/6 ENST00000375662.4:c.451+58dup 0.2731 0.3573 0.3581 0.3757 0.5051 0.5051 SAS TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01
0/0 2 6 6,0 6.0 6.0 0.0 0/1 2 6 4,2 6.0 50 PASS ZIC4 84107 . GRCh37 3 147121630 147121631 + Intron DEL TC TC - rs142316820 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 TC TC c.135+120_135+121del ENST00000525172 ZIC4,intron_variant,,ENST00000383075,NM_032153.5;ZIC4,intron_variant,,ENST00000425731,NM_001168379.1;ZIC4,intron_variant,,ENST00000462748,;ZIC4,intron_variant,,ENST00000463250,;ZIC4,intron_variant,,ENST00000473123,;ZIC4,intron_variant,,ENST00000484399,;ZIC1,intron_variant,,ENST00000488404,;ZIC4,intron_variant,,ENST00000491672,NM_001243256.1;ZIC4,intron_variant,,ENST00000525172,NM_001168378.1;ZIC4,upstream_gene_variant,,ENST00000484586,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,downstream_gene_variant,,ENST00000464144,; - ENSG00000174963 ENST00000525172 Transcript intron_variant rs142316820 1 -1 ZIC4 HGNC 20393 protein_coding YES CCDS54652.1 ENSP00000435509 Q8N9L1 C9JZU7,C9JD04,C9J6T3,B3KPI4 UPI0001914D88 NM_001168378.1 1/4 MODIFIER 1 deletion 1.0 PASS GATCT . 50 147121629 3_147121630_TC/- 3:147121630-147121631 - ENSG00000174963 ENST00000525172.2 Transcript intron_variant - - - - - rs142316820 IMPACT=MODIFIER;STRAND=-1;SYMBOL=ZIC4;SYMBOL_SOURCE=HGNC;HGNC_ID=20393;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS54652.1;ENSP=ENSP00000435509;SWISSPROT=Q8N9L1;TREMBL=C9JZU7,C9JD04,C9J6T3,B3KPI4;UNIPARC=UPI0001914D88;INTRON=1/4;HGVSc=ENST00000525172.2:c.135+120_135+121del MODIFIER -1 ZIC4 HGNC 20393 protein_coding YES CCDS54652.1 ENSP00000435509 Q8N9L1 UPI0001914D88 1/4 ENST00000525172.2:c.135+120_135+121del C9JZU7,C9JD04,C9J6T3,B3KPI4 TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01
0/0 2 7 7,0 7.0 7.0 0.0 0/1 2 6 2,4 6.0 50 PASS EIF4G1 1981 . GRCh37 3 184043926 184043927 + Intron DEL AC AC - rs34901174 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 AC AC c.3243+217_3243+218del ENST00000424196 EIF4G1,intron_variant,,ENST00000319274,;EIF4G1,intron_variant,,ENST00000342981,NM_182917.4;EIF4G1,intron_variant,,ENST00000346169,NM_198241.2;EIF4G1,intron_variant,,ENST00000350481,NM_198242.2;EIF4G1,intron_variant,,ENST00000352767,NM_001194947.1;EIF4G1,intron_variant,,ENST00000382330,NM_001194946.1;EIF4G1,intron_variant,,ENST00000392537,NM_198244.2;EIF4G1,intron_variant,,ENST00000411531,;EIF4G1,intron_variant,,ENST00000414031,;EIF4G1,intron_variant,,ENST00000424196,;EIF4G1,intron_variant,,ENST00000427845,;EIF4G1,intron_variant,,ENST00000434061,NM_004953.4;EIF4G1,intron_variant,,ENST00000435046,;EIF4G1,intron_variant,,ENST00000441154,;EIF2B5,intron_variant,,ENST00000444495,;EIF4G1,intron_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000421110,;EIF4G1,downstream_gene_variant,,ENST00000426123,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000428387,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000450424,;EIF4G1,downstream_gene_variant,,ENST00000457456,;SNORD66,downstream_gene_variant,,ENST00000390856,NR_003055.1;EIF4G1,intron_variant,,ENST00000442406,;EIF4G1,intron_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000413967,;EIF4G1,upstream_gene_variant,,ENST00000422614,;EIF4G1,upstream_gene_variant,,ENST00000460829,;EIF4G1,upstream_gene_variant,,ENST00000464548,;EIF4G1,upstream_gene_variant,,ENST00000475721,;EIF4G1,upstream_gene_variant,,ENST00000482303,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,downstream_gene_variant,,ENST00000493299,; - ENSG00000114867 ENST00000424196 Transcript intron_variant rs34901174 1 1 EIF4G1 HGNC 3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556 UPI00015E0966 20/31 MODIFIER 1 deletion 1.0 PASS AAACA rs112208190 50 184043925 rs112208190 3:184043926-184043927 - ENSG00000114867 ENST00000424196.1 Transcript intron_variant - - - - - rs34901174 IMPACT=MODIFIER;STRAND=1;SYMBOL=EIF4G1;SYMBOL_SOURCE=HGNC;HGNC_ID=3296;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS54687.1;ENSP=ENSP00000416255;SWISSPROT=Q04637;TREMBL=Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556;UNIPARC=UPI00015E0966;INTRON=20/31;HGVSc=ENST00000424196.1:c.3243+217_3243+218del MODIFIER 1 EIF4G1 HGNC 3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 UPI00015E0966 20/31 ENST00000424196.1:c.3243+217_3243+218del Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556 TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01
0/0 2 22 22,0 22.0 22.0 0.0 0/1 2 6 4,2 6.0 50 PASS STEAP1B 256227 . GRCh37 7 22533452 22533453 + Frame_Shift_Del DEL CA CA - novel TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 CA CA c.87_88del p.His29GlnfsTer24 p.H29Qfs*24 ENST00000404369 3/5 STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000404369,NM_001164460.1;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000424363,;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000439708,;STEAP1B,intron_variant,,ENST00000406890,NM_207342.2;STEAP1B,splice_region_variant,,ENST00000483679,; - ENSG00000105889 ENST00000404369 Transcript frameshift_variant,splice_region_variant 503-504/1515 87-88/1029 29-30/342 HE/QX caTGag/caag 1 -1 STEAP1B HGNC 41907 protein_coding YES CCDS56469.1 ENSP00000384370 C9JL51,C9JE84,B5MCI2 UPI000173A267 NM_001164460.1 3/5 PANTHER:PTHR14239:SF3,PANTHER:PTHR14239 HIGH 1 deletion PASS CTCAT rs116873396 50 22533451 rs116873396 7:22533452-22533453 - ENSG00000105889 ENST00000404369.4 Transcript frameshift_variant,splice_region_variant 503-504 87-88 29-30 HE/QX caTGag/caag - IMPACT=HIGH;STRAND=-1;SYMBOL=STEAP1B;SYMBOL_SOURCE=HGNC;HGNC_ID=41907;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS56469.1;ENSP=ENSP00000384370;TREMBL=C9JL51,C9JE84,B5MCI2;UNIPARC=UPI000173A267;EXON=3/5;HGVSc=ENST00000404369.4:c.87_88del;HGVSp=ENSP00000384370.4:p.His29GlnfsTer24 HIGH -1 STEAP1B HGNC 41907 protein_coding YES CCDS56469.1 ENSP00000384370 UPI000173A267 ENST00000404369.4:c.87_88del C9JL51,C9JE84,B5MCI2 3/5 ENSP00000384370.4:p.His29GlnfsTer24 TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01
0/0 2 31 31,0 31.0 31.0 0.0 0/1 2 6 4,2 6.0 50 PASS TEX12 56158 . GRCh37 11 112042480 112042480 + Intron DEL T T - rs1225064086 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 T T c.228-9del ENST00000280358 TEX12,intron_variant,,ENST00000280358,NM_031275.4;TEX12,intron_variant,,ENST00000530752,;AP002884.3,intron_variant,,ENST00000532612,;BCO2,upstream_gene_variant,,ENST00000357685,;BCO2,upstream_gene_variant,,ENST00000361053,NM_001256398.1;BCO2,upstream_gene_variant,,ENST00000393032,NM_031938.5;BCO2,upstream_gene_variant,,ENST00000438022,;BCO2,upstream_gene_variant,,ENST00000526088,NM_001037290.2,NM_001256397.1;BCO2,upstream_gene_variant,,ENST00000531169,;BCO2,upstream_gene_variant,,ENST00000532593,NM_001256400.1;RP11-356J5.4,intron_variant,,ENST00000527589,;SDHD,intron_variant,,ENST00000525468,;SDHD,intron_variant,,ENST00000525987,;SDHD,intron_variant,,ENST00000531744,;SDHD,intron_variant,,ENST00000532699,;BCO2,upstream_gene_variant,,ENST00000460924,;BCO2,upstream_gene_variant,,ENST00000461480,;BCO2,upstream_gene_variant,,ENST00000494860,;BCO2,upstream_gene_variant,,ENST00000527939,;BCO2,upstream_gene_variant,,ENST00000531003,;BCO2,upstream_gene_variant,,ENST00000534122,;BCO2,upstream_gene_variant,,ENST00000534550,; - ENSG00000150783 ENST00000280358 Transcript intron_variant rs1225064086 1 1 TEX12 HGNC 11734 protein_coding YES CCDS31679.1 ENSP00000280358 Q9BXU0 UPI00001377E3 NM_031275.4 4/4 MODIFIER 1 deletion PASS ACTT . 50 1.711e-05 8.319e-05 8.285e-05 1.133e-05 112042479 11_112042480_T/- 11:112042480 - ENSG00000150783 ENST00000280358.4 Transcript intron_variant - - - - - rs1225064086 IMPACT=MODIFIER;STRAND=1;SYMBOL=TEX12;SYMBOL_SOURCE=HGNC;HGNC_ID=11734;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS31679.1;ENSP=ENSP00000280358;SWISSPROT=Q9BXU0;UNIPARC=UPI00001377E3;INTRON=4/4;HGVSc=ENST00000280358.4:c.228-9del;gnomAD_AF=1.711e-05;gnomAD_AFR_AF=8.319e-05;gnomAD_AMR_AF=0;gnomAD_ASJ_AF=0;gnomAD_EAS_AF=8.285e-05;gnomAD_FIN_AF=0;gnomAD_NFE_AF=1.133e-05;gnomAD_OTH_AF=0;gnomAD_SAS_AF=0;MAX_AF=8.319e-05;MAX_AF_POPS=gnomAD_AFR MODIFIER 1 TEX12 HGNC 11734 protein_coding YES CCDS31679.1 ENSP00000280358 Q9BXU0 UPI00001377E3 4/4 ENST00000280358.4:c.228-9del 8.319e-05 gnomAD_AFR 1.711e-05 8.319e-05 0 0 8.285e-05 0 1.133e-05 0 0 TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01