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Input Formats

VNtyper 2 accepts BAM, CRAM, or paired-end FASTQ files as input. Provide exactly one input type per run.

vntyper pipeline --bam sample.bam -o results/

Requirements:

  • Sorted and indexed (.bam.bai or .bai must exist alongside the BAM)
  • Aligned to a supported reference assembly
  • VNtyper 2 validates the file with samtools quickcheck before processing
vntyper pipeline --cram sample.cram -o results/

Requirements:

  • Sorted and indexed (.cram.crai must exist)
  • Aligned to a supported reference assembly
  • The original reference FASTA must be accessible (CRAM files are reference-dependent)
  • Validated with samtools quickcheck
vntyper pipeline --fastq1 R1.fastq.gz --fastq2 R2.fastq.gz -o results/

Requirements:

  • Paired-end reads: both --fastq1 and --fastq2 are required
  • Gzipped (.fastq.gz) or uncompressed (.fastq) accepted
  • VNtyper 2 validates FASTQ format (checks first 4 lines for correct structure)
  • Reads are processed through fastp for quality control, then aligned with BWA

SHARK module requires FASTQ input

The SHARK filtering module (--extra-modules shark) only works with FASTQ input. With BAM or CRAM input, the SHARK module is silently skipped even if specified.

Input Validation

VNtyper 2 performs automatic validation before starting the pipeline:

Input Type Validation Method
BAM / CRAM samtools quickcheck -- verifies file integrity and EOF marker
FASTQ Format check -- verifies the first 4 lines follow FASTQ structure

If validation fails, the pipeline exits immediately with a descriptive error message.