picard_reordersam

picard_reordersam reorders Sequence Alignment/Map (SAM) and Binary Alignment/Map (BAM) files to match the contig ordering of a specified reference file for downstream genomic analyses.

Key Features:

• Exact Name Matching: Reorders reads according to exact contig or chromosome name matches between the input SAM/BAM and the specified reference.
• Exclusion of Non-Matching Reads: Omits reads mapped to contigs that are not present in the provided reference from the output file.
• Complementary to SortSam: Performs name-based reordering distinct from SortSam, which sorts by coordinate values or query names.

Scientific Applications:

• Comparative Genomics: Ensures alignment files use a consistent contig order for comparative analyses across references or samples.
• Variant Calling: Provides contig-order consistency required by variant-calling workflows that depend on a specific reference ordering.
• Reference Version Control and Custom Assemblies: Prevents discrepancies arising from different reference versions or custom assemblies by matching contig order to a target reference.
• Next-Generation Sequencing Data Processing: Supports accurate downstream analyses of high-throughput sequencing datasets by aligning file contig order to the chosen reference.

Methodology:

Parses input SAM/BAM files, matches read mappings to contig/chromosome names in the specified reference, reorders reads to mirror the reference contig order, and excludes reads mapped to contigs absent from the reference.