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Bamtofastq Samtools Fastq Specifications

Process Details

  • Name: bamtofastq_samtools_fastq
  • Process UUID: lx0CXxFZiI4ijSdfjOzw29gp9Jzecu
  • Process Group: Misc.

Overview

This process converts BAM files to FASTQ format while automatically determining whether the sequencing data is single-end or paired-end. The process sorts BAM files by read name for optimal downstream processing and handles both compressed and uncompressed input files.

This process is implemented in Bash, which uses samtools for BAM file manipulation and format conversion.

Key Functionality

  • BAM to FASTQ Conversion: Converts aligned BAM files back to FASTQ format for reprocessing or alternative analysis workflows
  • Automatic Pairing Detection: Determines whether the input data is single-end or paired-end sequencing and processes accordingly
  • Name-based Sorting: Sorts BAM files by read name to ensure proper pairing in paired-end data
  • Compression Handling: Automatically decompresses gzipped BAM files and compresses output FASTQ files

Input/Output Specification

Inputs

Required Inputs

  • mate
    • Description: Mate information parameter for processing context
    • Format: mate parameter

Optional Inputs

  • reads

    • Description: FASTQ reads (when available)
    • Format: FASTQ files

  • bamFile

    • Description: BAM alignment files to be converted to FASTQ format
    • Format: BAM files (compressed or uncompressed)

Outputs

  • reads

    • Description: Converted FASTQ files, either single-end (.fastq) or paired-end (.R1.fastq, .R2.fastq)
    • Format: Gzipped FASTQ files

  • mate

    • Description: Environment variable indicating whether data is single-end or paired-end
    • Format: Environment parameter (single/pair)

Parameters & Settings

No user-configurable parameters are available for this process in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on the samtools implementation used in this process