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

Description of special things here

• 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