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splitNCigarReads Specifications

Process Details

  • Name: splitNCigarReads
  • Process UUID: f931gyge0t6ssbj9esfpit26rh8uof
  • Process Group: gatk4

Overview

This process performs split N-CIGAR reads operation using GATK4's SplitNCigarReads tool. It processes BAM files containing RNA-seq alignments to split reads that span introns, which is essential for variant calling on RNA-seq data. The tool handles reads with N operations in their CIGAR strings by splitting them into separate alignment segments.

This process is implemented in Bash, which invokes GATK4 for genomic data processing.

Key Functionality

  • Split N-CIGAR Reads: Splits reads with N operations in CIGAR strings into separate alignment segments
  • RNA-seq Preprocessing: Prepares RNA-seq BAM files for downstream variant calling analysis
  • Reference-based Processing: Uses genome reference dictionary for proper coordinate handling

Input/Output Specification

Inputs

Required Inputs

  • BAM File

    • Description: Set of BAM files containing aligned RNA-seq reads with potential N-CIGAR operations
    • Format: BAM

  • Genome Dictionary

    • Description: Reference genome dictionary file required for GATK operations
    • Format: DICT

Outputs

  • BAM File
    • Description: Set of processed BAM files with split N-CIGAR reads suitable for variant calling
    • Format: BAM

Parameters & Settings

This process uses default GATK4 SplitNCigarReads parameters and does not expose user-configurable options in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on GATK4 SplitNCigarReads functionality
  • Related Papers: McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20, 1297-1303 (2010). DOI: 10.1101/gr.107524.110