HGVS and t_alt ann using GATK.GRCh38

[allyssonallan]

Description of the bug

Hey @famosab thanks for your amazing support. I was trying to recover the annotation made by snpEff and VEP (merge option) in vcf2maf and I'd like to share this option in config that made by day. Also, I'd like to ask if these default params are related to the hg19 input, because I can't work with current hg38 vcf annotated structure from somatic sarek.

Here: conf/modules.config

I changed the

"--retain-info HGVSp_VEP,HGVSc_VEP,genename,codonpos,clinvar_hgvs,cds_strand,aaref,aaalt,aapos,VEP_canonical,MutPred_AAchange",
 "--retain-ann HGVSp_VEP,HGVSc_VEP,genename,codonpos,clinvar_hgvs,cds_strand,aaref,aaalt,aapos,VEP_canonical,MutPred_AAchange",
"--retain-fmt HGVSp_VEP,HGVSc_VEP,genename,codonpos,clinvar_hgvs,cds_strand,aaref,aaalt,aapos,VEP_canonical,MutPred_AAchange ",

To

˜--retain-fmt AD,AF,DP,GQ,GT,STR˜,
˜--retain-info AS_FilterStatus,AS_SB_TABLE,DP,MBQ,POPAF,STR,ANN,LOF,NMD˜,
˜--retain-ann Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,CDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,MANE_SELECT,MANE_PLUS_CLINICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AFIgnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF,gnomADg_EAS_AF_POPS,FREQS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,TRANSCRIPTION_FACTORS˜,

And it worked.

Relevant files

Before:

After:

[allyssonallan]

I followed your suggestion @FriederikeHanssen Thanks! :)

mskcc/vcf2maf#346

[famosab]

I think you are right, @allyssonallan - this config is related to hg19. I can change the configuration the way you suggested. Is there anything else that you modified?

[allyssonallan]

Perfect @famosab Super thanks :)