Input Files

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