Input Files for ANSWER

Manifest File

Data Files

  • VCF File for all samples (Tumor/Normal)

  • Special Variables in the INFO field (most of optional)

  • ANN: SNPEff Annotation

  • DP: Tumor Read Depth (not optional)

  • AF: Tumor Mutational Allele Frequency (not optional)

  • NormalDP: Normal Read Depth

  • NormalAF: Normal Mutational Allele Frequency

  • RNASeqDP: Normal Read Depth

  • RNASeqAF: Normal Mutational Allele Frequency

  • CallSet: Algorithm used to predict variant

  • GNOMAD_AF: GNOMAD POPMAX

  • GNOMAD_HG19_VARIANT: chr-pos-ref-alt to link to GNOMAD website

  • GNOMAD_HOM: Number of homozygous samples in GNOMAD

  • CNV Files

  • CNR: Bait Coverage Files (example.answerplot.cnr)

  • CNS: Segment Coverage Files (example.answerplot.cns)

  • TXT: Copy Number Prediction File (example.cnv.answer.txt)

  • B-Allele Freq: File of Common SNP B-Allele Frequency File (example.ballelefreq.txt)

  • Viral Results (tab-delimited see example.viral_results.txt)

  • SampleID: Tumor or Normal Sample ID

  • VirusName: Short Name for Virus

  • VirusAcc: Refseq Genome ID

  • VirusDescription: Genome Name

  • ViralReadCt: Number of Reads

  • TMB (csv see example.TMB.csv)

  • Metric: TMB or MSI

  • Value: Score

  • Class: Classification of Score ie TMB-High or MSS

  • Mutational Signature Files

  • TXT File

  • PNG File

  • RNA Files

    • FPKM Gene Abundance File

    • Translocation/Gene Fusion File

    • Exons Skipping

  • TN Concordance File

Alignment Files for IGV

  • Tumor DNA BAM and BAI

  • Normal DNA BAM and BAI

  • Tumor RNA BAM and BAI

Cbioportal Files

  • Somatic MAF