Skip to content

Input Formats

gbcms accepts VCF and MAF files as variant input.

VCF (Variant Call Format)

Standard VCF format with required fields:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr1    12345   .       A       T       .       PASS    .
chr2    67890   .       G       C       .       PASS    .

Requirements

  • Tab-separated
  • #CHROM, POS, REF, ALT columns required
  • 1-based positions

MAF (Mutation Annotation Format)

Standard MAF format with required columns:

Hugo_Symbol  Chromosome  Start_Position  End_Position  Reference_Allele  Tumor_Seq_Allele2
TP53         chr17       7577120         7577120       C                 T
KRAS         chr12       25398284        25398284      G                 A

Required Columns

Column Description
Chromosome Chromosome name
Start_Position 1-based start position
Reference_Allele Reference allele
Tumor_Seq_Allele2 Alternate allele

MAF Indel Normalization

MAF represents indels using - dashes, while gbcms internally uses VCF-style anchor-based coordinates. When a MAF file contains insertions (Reference_Allele = -) or deletions (Tumor_Seq_Allele2 = -), gbcms automatically converts them at input time.

Reference FASTA Required

MAF indel conversion requires --fasta to fetch the anchor base from the reference genome. Without it, indel variants cannot be normalized and will be skipped.

flowchart TD
    MAF(["📄 MAF Row"]):::start --> Check{"REF or ALT is '-'?"}
    Check -->|"No — SNP/MNP"| Direct["VCF POS = Start_Position"]
    Check -->|"Yes — Indel"| Type{"Which is '-'?"}

    Type -->|"REF = '-' (Insertion)"| InsResult["POS = Start_Position\nAnchor @ Start_Position (from FASTA)\nREF = anchor\nALT = anchor + inserted seq"]
    Type -->|"ALT = '-' (Deletion)\n-1 for anchor"| DelResult["POS = Start_Position − 1\nAnchor @ Start_Position−1 (from FASTA)\nREF = anchor + deleted seq\nALT = anchor"]

    Direct --> Out(["🧬 Internal Variant"]):::pass
    InsResult --> Out
    DelResult --> Out

    classDef start fill:#9b59b6,color:#fff,stroke:#7d3c98,stroke-width:2px;
    classDef pass fill:#27ae60,color:#fff,stroke:#1e8449,stroke-width:2px;
Use mouse to pan and zoom

Insertion Example

Insert TG after chr1:100 (where the reference base at position 100 is A):

Field MAF VCF (internal)
Position Start_Position = 100 POS = 100
REF - A (fetched from FASTA)
ALT TG ATG (anchor + inserted seq)

Deletion Example

Delete CG at chr1:101–102 (where the reference base at position 100 is A):

Field MAF VCF (internal)
Position Start_Position = 101 (first deleted base) POS = 100 (anchor)
REF CG ACG (anchor + deleted seq)
ALT - A (anchor only)

Position Shift for Deletions

For insertions, Start_Position already points to the anchor base. For deletions, Start_Position points to the first deleted base, so gbcms shifts back by one position to find the anchor.

Variant Left-Normalization

gbcms automatically left-aligns indels and complex variants during the preparation step. For full details on the normalization algorithm, homopolymer decomposition detection, and REF validation, see Variant Normalization.

Left-Align Your Variants

Inconsistently normalized variants reduce the effectiveness of windowed indel detection. While the ±5bp window will catch most aligner-shifted indels, left-alignment ensures the anchor position is consistent with standard conventions.

# VCF: use bcftools norm
bcftools norm -f reference.fa -o normalized.vcf input.vcf

Reference FASTA

  • Must have corresponding .fai index
  • Chromosome names must match VCF/MAF
# Create index if missing
samtools faidx reference.fa

BAM Requirements

  • Must have corresponding .bai index
  • Coordinate-sorted
  • Chromosome names must match reference