snv_extractor_v1.pl wont work with VEP annotations

[kubranarci]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

nf-snvcalling pipeline is hard-coded to wotk with ANNOVAR annotations. We were testing the pipeline to work with VEP as well, yet, I discover some ANNOVAR annotations are required for snv_extractor_v1.pl to extract high confidence variants.

missing headers: ANNOVAR_FUNCTION, GENE, EXONIC_CLASSIFICATION, ANNOVAR_TRANSCRIPTS,SEGDUP, CYTOBAND

among them, ANNOVAR_FUNCTION is being used to decide if variants function (ninsynonmous,ncRNA_splicing,stopgain,ncRNA_exonic,stoploss,splicing etc)

Command used and terminal output

No response

Relevant files

VEP
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HCC1187-T-D1.recal.cram SEQUENCE_CONTEXT INFO_control(VAF=variant_allele_fraction;TSR=total_variant_supporting_reads_incl_lowqual) ANNOTATION_control DBSNP 1K_GENOMES LocalControlAF_WGS LocalControlAF_WES GNOMAD_GENOMES GNOMAD_EXOMES REPEAT_MASKER MAPABILITY SIMPLE_TANDEMREPEATS CONFIDENCE RECLASSIFICATION
chr1 852359 rs369182284 G A 33.0091 PASS DP=14;VDB=0.206307;SGB=-0.511536;RPB=0.177538;MQB=0.0608101;MQSB=0.695312;BQB=0.040184;MQ0F=0;AF1=0.5;AC1=1;DP4=4,5,2,1;MQ=48;FQ=36.0162;PV4=0.559441,1,0.0111843,0.0779648;CSQ=A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918352|enhancer||||||||||rs369182284||||SNV|||||||||||||||||||||||||||||||||||0.002884|0.005987|0.001119|0.002378|0.003395|0.0007871|0.0008667|0|0.001691|0.002541|0.003949|0.005987|gnomADg_AFR||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01128|ENSG00000228794|Transcript|ENST00000445118|lncRNA||3/4|ENST00000445118.7:n.464+249G>A|||||||rs369182284||1||SNV|HGNC|HGNC:49377|YES|||1|||||||||||||||||||||||||||||0.002884|0.005987|0.001119|0.002378|0.003395|0.0007871|0.0008667|0|0.001691|0.002541|0.003949|0.005987|gnomADg_AFR||||||||||;ACGTNacgtnPLUS=2,0,2,0,0,0,0,4,0,0;ACGTNacgtnMINUS=0,0,2,0,0,1,0,2,0,0;DP4original=4,6,2,1;DP2sup=0,0;DP2dup=0,0;DP2pairEnd=1,0;DP2mis=0,0;DP2nonREFnonALT=0,0;MAFCommon GT:PL:AD 0/1:63,0,175:10,3 GTTGGCTTCC,TGACTGGTCA DP=14;DP5=6,8,0,0,0;DP5all=6,8,0,0,0;ACGTNacgtnHQ=0,0,6,0,0,0,0,8,0,0;ACGTNacgtn=0,0,6,0,0,0,0,8,0,0;VAF=0.00;TSR=0;PBINOM=6.103515625e-05 somatic MATCH=exact;RS=369182284;RSPOS=852359;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050100080005000002000100;GENEINFO=LINC01128:643837;WGT=1;VC=SNV;SLO;INT;ASP;TOPMED=0.99259365443425076,0.00740634556574923;ID=rs369182284 MATCH=exact;AC=289;AN=5096;DP=23679;AF=0.06;EAS_AF=0.02;EUR_AF=0.03;AFR_AF=0.13;AMR_AF=0.03;SAS_AF=0.04;VT=SNP;NS=2548;ID=. MATCH=exact;AC=163;AF=0.0334084853453577;AN=4879;VAFc=0.128569451651963;VAFt=0.0869805194805195;PassF=0.220555;HOMO=0;SOURCE=HIPO,PCAWG . MATCH=exact;AC=414;AN=134762;AF=0.0030720799695700407;fAF_95=0.0028275800868868828;fAF_99=0.0028273900970816612;AF_afr=0.006112670060247183;AF_amr=0.002433090005069971;AF_eas=0.0009848979534581304;AF_fin=0.0008783920202404261;AF_nfe=0.0017492600018158555;AF_sas=0.005598320160061121;AF_oth=0.0034584999084472656;HOMO=0;HOMO_nfe=0;HOMO_sas=0;FILTER=PASS . . 0.5 . 8 SNP_support_germline

ANNOVAR:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HCC1187-T-D1.recal.cram SEQUENCE_CONTEXT INFO_control(VAF=variant_allele_fraction;TSR=total_variant_supporting_reads_incl_lowqual) ANNOTATION_control DBSNP 1K_GENOMES LocalControlAF_WGS LocalControlAF_WES GNOMAD_GENOMES GNOMAD_EXOMES ANNOVAR_FUNCTION GENE EXONIC_CLASSIFICATION ANNOVAR_TRANSCRIPTS SEGDUP CYTOBAND REPEAT_MASKER MAPABILITY SIMPLE_TANDEMREPEATS CONFIDENCE RECLASSIFICATION
chr1 852359 rs369182284 G A 33.0091 PASS DP=14;VDB=0.206307;SGB=-0.511536;RPB=0.177538;MQB=0.0608101;MQSB=0.695312;BQB=0.040184;MQ0F=0;AF1=0.5;AC1=1;DP4=4,5,2,1;MQ=48;FQ=36.0162;PV4=0.559441,1,0.0111843,0.0779648;ACGTNacgtnPLUS=2,0,2,0,0,0,0,4,0,0;ACGTNacgtnMINUS=0,0,2,0,0,1,0,2,0,0;DP4original=4,6,2,1;DP2sup=0,0;DP2dup=0,0;DP2pairEnd=1,0;DP2mis=0,0;DP2nonREFnonALT=0,0;MAFCommon GT:PL:AD 0/1:63,0,175:10,3 GTTGGCTTCC,TGACTGGTCADP=14;DP5=6,8,0,0,0;DP5all=6,8,0,0,0;ACGTNacgtnHQ=0,0,6,0,0,0,0,8,0,0;ACGTNacgtn=0,0,6,0,0,0,0,8,0,0;VAF=0.00;TSR=0;PBINOM=6.103515625e-05 somatic MATCH=exact;RS=369182284;RSPOS=852359;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050100080005000002000100;GENEINFO=LINC01128:643837;WGT=1;VC=SNV;SLO;INT;ASP;TOPMED=0.99259365443425076,0.00740634556574923;ID=rs369182284 MATCH=exact;AC=289;AN=5096;DP=23679;AF=0.06;EAS_AF=0.02;EUR_AF=0.03;AFR_AF=0.13;AMR_AF=0.03;SAS_AF=0.04;VT=SNP;NS=2548;ID=. MATCH=exact;AC=163;AF=0.0334084853453577;AN=4879;VAFc=0.128569451651963;VAFt=0.0869805194805195;PassF=0.220555;HOMO=0;SOURCE=HIPO,PCAWG . MATCH=exact;AC=414;AN=134762;AF=0.0030720799695700407;fAF_95=0.0028275800868868828;fAF_99=0.0028273900970816612;AF_afr=0.006112670060247183;AF_amr=0.002433090005069971;AF_eas=0.0009848979534581304;AF_fin=0.0008783920202404261;AF_nfe=0.0017492600018158555;AF_sas=0.005598320160061121;AF_oth=0.0034584999084472656;HOMO=0;HOMO_nfe=0;HOMO_sas=0;FILTER=PASS . ncRNA_exonic LINC01128 . . Score=0.97802;Name=chr8:290489 1p36.33 . 0.5 . 8 SNP_support_germline

System information

No response