Input Formats

py-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

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

Related

• CLI Run Command — Usage examples

• Architecture — How counting works

• Glossary — Term definitions