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Choose Your Mode

gbcms supports two sequencing contexts. Pick the one that matches your data — the rest of the setup follows from there.

flowchart TD
    Start(["What sequencing data?"]):::start

    Start -->|"cfDNA · IMPACT · WGS\nWES · Panel"| DNA(["gbcms dna"]):::dna
    Start -->|"STAR-aligned RNA-seq\ndUTP stranded"| RNA(["gbcms rna"]):::rna
    Start -->|"Unstranded RNA-seq\n(random orientation)"| RNAL(["gbcms rna\n--strandedness unstranded"]):::rnal

    classDef start fill:#9b59b6,color:#fff,stroke:#7d3c98,stroke-width:2px;
    classDef dna fill:#27ae60,color:#fff,stroke:#1e8449,stroke-width:2px;
    classDef rna fill:#3498db,color:#fff,stroke:#2471a3,stroke-width:2px;
    classDef rnal fill:#2471a3,color:#fff,stroke:#1a5276,stroke-width:2px;
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Use for: cfDNA (MSK-ACCESS, IMPACT), WGS, WES, targeted gene panels

Key capabilities:

  • Windowed indel detection with 3-layer safeguards (±5bp, adaptively extended in repeats)
  • Mutant Fragment Size Distribution (--mfsd) for short-fragment enrichment analysis
  • UMI-aware fragment deduplication (--umi-tag)
  • Multi-allelic sibling exclusion to prevent REF inflation at complex loci

Defaults: MAPQ 20 · base quality 20 · duplicates filtered · PairHMM standard gap penalties

→ Quick Start | Full CLI Reference

Use for: STAR-aligned RNA-seq (dUTP stranded or unstranded)

Key capabilities:

  • NH:i:1 rescue of uniquely aligned reads whose MAPQ falls below --min-mapq; MAPQ 1 default keeps STAR's two-to-four-locus primaries
  • dUTP strandedness filtering (--strandedness unstranded for unstranded libraries; forward for fr-secondstrand)
  • A-to-I RNA editing site flagging via REDIportal (--rna-editing-db)
  • Splice junction tracking (rna_splice_spanning)

Defaults: MAPQ 1 · base quality 20 · secondary/supplementary/QC-failed reads filtered · PairHMM relaxed RT gap penalties

→ Quick Start | Full CLI Reference

Prerequisites

Requirement DNA RNA
Python 3.10+ ✅ ✅
BAM file with .bai index ✅ ✅
Reference FASTA with .fai index ✅ ✅
VCF or MAF with variant positions ✅ ✅
STAR-aligned BAM (NH tag) — ✅
GTF annotation (--gtf), the source of each variant's gene strand — Needed for strand-aware counting
REDIportal TABLE1 file — Optional

BAM Index

If your BAM lacks an index: samtools index sample.bam

FASTA Index

If your FASTA lacks an index: samtools faidx reference.fa