Commit c7717d8c authored by Pradat Yoann's avatar Pradat Yoann

remove gitlab ci; add badges

parent 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
......@@ -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
......
# 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
......
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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
0/0 2 48 48,0 48.0 48.0 0.0 0/1 2 33 26,7 33.0 50 PASS KMT2D 8085 . GRCh37 12 49431403 49431404 + Frame_Shift_Ins INS - - T novel TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 - - c.9735dup p.Pro3246ThrfsTer5 p.P3246Tfs*5 ENST00000301067 34/54 KMT2D,frameshift_variant,p.Pro3246ThrfsTer5,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,; T ENSG00000167548 ENST00000301067 Transcript frameshift_variant 9735-9736/19419 9735-9736/16614 3245-3246/5537 -/X -/A 1 -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 NM_003482.3 34/54 PANTHER:PTHR22884,PANTHER:PTHR22884:SF324 HIGH 1 insertion 1.0 PASS GGT . 50 49431403 12_49431404_-/T 12:49431403-49431404 T ENSG00000167548 ENST00000301067.7 Transcript frameshift_variant 9735-9736 9735-9736 3245-3246 -/X -/A - IMPACT=HIGH;STRAND=-1;SYMBOL=KMT2D;SYMBOL_SOURCE=HGNC;HGNC_ID=7133;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS44873.1;ENSP=ENSP00000301067;SWISSPROT=O14686;TREMBL=Q6PIA1,Q59FG6,F8VWW4;UNIPARC=UPI0000EE84D6;EXON=34/54;HGVSc=ENST00000301067.7:c.9735dup;HGVSp=ENSP00000301067.7:p.Pro3246ThrfsTer5 HIGH -1 KMT2D HGNC 7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 ENST00000301067.7:c.9735dup Q6PIA1,Q59FG6,F8VWW4 34/54 ENSP00000301067.7:p.Pro3246ThrfsTer5 TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01
0/0 2 47 47,0 47.0 47.0 0.0 0/1 2 6 4,2 6.0 50 PASS PDS5B 23047 . GRCh37 13 33332314 33332314 + Frame_Shift_Del DEL A A - novel TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 A A c.3148del p.Thr1050GlnfsTer12 p.T1050Qfs*12 ENST00000315596 27/35 PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000315596,NM_015032.3;PDS5B,frameshift_variant,p.Thr4GlnfsTer12,ENST00000447833,;PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000450460,; - ENSG00000083642 ENST00000315596 Transcript frameshift_variant 3332/7497 3146/4344 1049/1447 Q/X cAa/ca 1 1 PDS5B HGNC 20418 protein_coding YES CCDS41878.1 ENSP00000313851 Q9NTI5 UPI000006D4A9 NM_015032.3 27/35 PANTHER:PTHR12663,PANTHER:PTHR12663:SF1 HIGH 1 deletion 2.0 PASS ACAA . 50 33332313 13_33332314_A/- 13:33332314 - ENSG00000083642 ENST00000315596.10 Transcript frameshift_variant 3332 3146 1049 Q/X cAa/ca - IMPACT=HIGH;STRAND=1;SYMBOL=PDS5B;SYMBOL_SOURCE=HGNC;HGNC_ID=20418;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS41878.1;ENSP=ENSP00000313851;SWISSPROT=Q9NTI5;UNIPARC=UPI000006D4A9;EXON=27/35;HGVSc=ENST00000315596.10:c.3148del;HGVSp=ENSP00000313851.10:p.Thr1050GlnfsTer12;HGVS_OFFSET=2 HIGH 1 PDS5B HGNC 20418 protein_coding YES CCDS41878.1 ENSP00000313851 Q9NTI5 UPI000006D4A9 ENST00000315596.10:c.3148del 27/35 ENSP00000313851.10:p.Thr1050GlnfsTer12 2 TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01
0/0 2 5 5,0 5.0 5.0 0.0 0/1 2 6 4,2 6.0 50 PASS CCR7 1236 . GRCh37 17 38712161 38712161 + Intron DEL T T - rs372297045 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 T T c.61-91del ENST00000246657 CCR7,intron_variant,,ENST00000246657,NM_001838.3;CCR7,intron_variant,,ENST00000578085,;CCR7,intron_variant,,ENST00000579344,; - ENSG00000126353 ENST00000246657 Transcript intron_variant rs372297045 1 -1 CCR7 HGNC 1608 protein_coding YES CCDS11369.1 ENSP00000246657 P32248 J3KTN5,J3KSS9,A0N0Q0 UPI0000001C2F NM_001838.3 2/2 0.004 MODIFIER 1 deletion 1.0 PASS TCTT . 50 38712160 17_38712161_T/- 17:38712161 - ENSG00000126353 ENST00000246657.2 Transcript intron_variant - - - - - rs372297045 IMPACT=MODIFIER;STRAND=-1;SYMBOL=CCR7;SYMBOL_SOURCE=HGNC;HGNC_ID=1608;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS11369.1;ENSP=ENSP00000246657;SWISSPROT=P32248;TREMBL=J3KTN5,J3KSS9,A0N0Q0;UNIPARC=UPI0000001C2F;INTRON=2/2;HGVSc=ENST00000246657.2:c.61-91del;AFR_AF=0;AMR_AF=0;EAS_AF=0.004;EUR_AF=0;SAS_AF=0;MAX_AF=0.004;MAX_AF_POPS=EAS MODIFIER -1 CCR7 HGNC 1608 protein_coding YES CCDS11369.1 ENSP00000246657 P32248 UPI0000001C2F 2/2 ENST00000246657.2:c.61-91del 0 0 0.004 0 0 0.004 EAS J3KTN5,J3KSS9,A0N0Q0 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 15 9,6 15.0 50 PASS ATP9A 10079 . GRCh37 20 50342307 50342308 + Intron DEL TC TC - novel TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 TC TC c.327+50_327+51del ENST00000338821 ATP9A,intron_variant,,ENST00000311637,;ATP9A,intron_variant,,ENST00000338821,NM_006045.1;ATP9A,intron_variant,,ENST00000402822,;ATP9A,downstream_gene_variant,,ENST00000477492,;,regulatory_region_variant,,ENSR00001644001,; - ENSG00000054793 ENST00000338821 Transcript intron_variant 1 -1 ATP9A HGNC 13540 protein_coding YES CCDS33489.1 ENSP00000342481 O75110 Q2NLD0,B4DR18 UPI000004D334 NM_006045.1 3/27 MODIFIER 1 deletion PASS TTTCT . 50 50342306 20_50342307_TC/- 20:50342307-50342308 - ENSG00000054793 ENST00000338821.5 Transcript intron_variant - - - - - - IMPACT=MODIFIER;STRAND=-1;SYMBOL=ATP9A;SYMBOL_SOURCE=HGNC;HGNC_ID=13540;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS33489.1;ENSP=ENSP00000342481;SWISSPROT=O75110;TREMBL=Q2NLD0,B4DR18;UNIPARC=UPI000004D334;INTRON=3/27;HGVSc=ENST00000338821.5:c.327+50_327+51del MODIFIER -1 ATP9A HGNC 13540 protein_coding YES CCDS33489.1 ENSP00000342481 O75110 UPI000004D334 3/27 ENST00000338821.5:c.327+50_327+51del Q2NLD0,B4DR18 TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01
n_GT n_SS n_FA n_DP n_AD t_GT t_SS t_FA t_DP t_AD Variant_Quality Filter_VCF Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER flanking_bps vcf_id vcf_qual ExAC_AF_Adj ExAC_AC_AN_Adj ExAC_AC_AN ExAC_AC_AN_AFR ExAC_AC_AN_AMR ExAC_AC_AN_EAS ExAC_AC_AN_FIN ExAC_AC_AN_NFE ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF vcf_pos Tumor_Sample Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Tumor_Sample_Site
0/0 2 0.0 69 69,0 0/1 2 0.276 58 42,16 43 PASS SLC6A9 6536 . GRCh37 1 44476442 44476442 + Missense_Mutation SNP C C T C C c.362G>A p.Gly121Asp p.G121D ENST00000360584 3/14 58 42 16 69 69 0 SLC6A9,missense_variant,p.Gly48Asp,ENST00000372310,NM_001024845.2;SLC6A9,missense_variant,p.Gly121Asp,ENST00000360584,NM_201649.3;SLC6A9,missense_variant,p.Gly67Asp,ENST00000357730,NM_006934.3,NM_001261380.1;SLC6A9,missense_variant,p.Gly48Asp,ENST00000372306,;SLC6A9,missense_variant,p.Gly102Asp,ENST00000466926,;SLC6A9,missense_variant,p.Gly67Asp,ENST00000528803,;SLC6A9,5_prime_UTR_variant,,ENST00000372307,;SLC6A9,intron_variant,,ENST00000475075,;SLC6A9,intron_variant,,ENST00000537678,;SLC6A9,intron_variant,,ENST00000492434,;SLC6A9,downstream_gene_variant,,ENST00000533007,;SLC6A9,non_coding_transcript_exon_variant,,ENST00000489764,; T ENSG00000196517 ENST00000360584 Transcript missense_variant 554/2330 362/2121 121/706 G/D gGc/gAc COSV62211565 1 -1 SLC6A9 HGNC 11056 protein_coding YES CCDS41317.1 ENSP00000353791 P48067 B7Z589 UPI000053030B NM_201649.3 deleterious(0) probably_damaging(1) 3/14 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,PANTHER:PTHR11616:SF110,PANTHER:PTHR11616,Pfam:PF00209,Superfamily:0053687,Prints:PR00176 1 MODERATE 1.0 SNV 1 1.0 PASS GCC . 43 44476442 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
0/0 2 0.0 77 77,0 0/1 2 0.083 36 33,3 6 PASS ADSS 159 . GRCh37 1 244583577 244583577 + Missense_Mutation SNP G G T novel G G c.685C>A p.Pro229Thr p.P229T ENST00000366535 8/13 36 33 3 77 77 0 ADSS,missense_variant,p.Pro229Thr,ENST00000366535,NM_001126.3;ADSS,non_coding_transcript_exon_variant,,ENST00000462358,;ADSS,upstream_gene_variant,,ENST00000468215,; T ENSG00000035687 ENST00000366535 Transcript missense_variant 1002/2780 685/1371 229/456 P/T Cca/Aca 1 -1 ADSS HGNC 292 protein_coding YES CCDS1624.1 ENSP00000355493 P30520 UPI0000132AF5 NM_001126.3 deleterious(0.02) probably_damaging(0.983) 8/13 HAMAP:MF_00011,HAMAP:MF_03127,PANTHER:PTHR11846:SF1,PANTHER:PTHR11846,Gene3D:2v40A01,TIGRFAM:TIGR00184,Pfam:PF00709,SMART:SM00788,Superfamily:SSF52540 MODERATE 1.0 SNV PASS GGT . 6 244583577 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
0/0 2 0.0 33 33,0 0/1 2 0.47100000000000003 17 9,8 24 PASS DTNB 1838 . GRCh37 2 25678299 25678299 + Missense_Mutation SNP C C T rs1230449080 C C c.1144G>A p.Val382Met p.V382M ENST00000406818 11/21 17 9 8 33 33 0 DTNB,missense_variant,p.Val382Met,ENST00000406818,NM_001256303.1,NM_021907.4;DTNB,missense_variant,p.Val382Met,ENST00000407661,NM_183360.2,NM_001256304.1;DTNB,missense_variant,p.Val382Met,ENST00000404103,NM_033147.3;DTNB,missense_variant,p.Val382Met,ENST00000288642,;DTNB,missense_variant,p.Val325Met,ENST00000496972,NM_001256308.1;DTNB,missense_variant,p.Val178Met,ENST00000545439,;DTNB,intron_variant,,ENST00000405222,NM_183361.2;DTNB,intron_variant,,ENST00000407038,NM_033148.3;DTNB,intron_variant,,ENST00000407186,;DTNB,intron_variant,,ENST00000481841,;DTNB,intron_variant,,ENST00000486555,;DTNB,intron_variant,,ENST00000489756,;DTNB,3_prime_UTR_variant,,ENST00000398951,;DTNB,non_coding_transcript_exon_variant,,ENST00000485845,;DTNB,non_coding_transcript_exon_variant,,ENST00000479898,;DTNB,intron_variant,,ENST00000356599,;DTNB,intron_variant,,ENST00000482145,; T ENSG00000138101 ENST00000406818 Transcript missense_variant 1394/2474 1144/1884 382/627 V/M Gtg/Atg rs1230449080,COSV56481440 1 -1 DTNB HGNC 3058 protein_coding YES CCDS46237.1 ENSP00000384084 O60941 Q53TC8,Q53T51,Q53SF9,Q53QV1,F8W9U0,E9PE76,E7ES64 UPI0000129949 NM_001256303.1,NM_021907.4 deleterious(0.03) benign(0.379) 11/21 PANTHER:PTHR11915:SF227,PANTHER:PTHR11915,PIRSF:PIRSF038204 0,1 MODERATE 1.0 SNV 0,1 PASS ACA . 24 25678299 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
0/0 2 0.0 50 50,0 0/1 2 0.514 37 18,19 56 PASS CADM2 253559 . GRCh37 3 85932472 85932472 + Silent SNP C