genome-read-alignment

name	genome-read-alignment
description	Align short reads to a reference genome with BWA-MEM2, sort and index with samtools, and mark duplicates with picard.

Skill: genome-read-alignment

Use When

• User needs to align FASTQ reads to a reference genome.
• User wants to produce a coordinate-sorted, indexed BAM file.
• User needs to mark PCR or optical duplicates in aligned reads.
• User wants to add read group information (@RG) to alignments.

Inputs

• Required:
  • Trimmed FASTQ file(s) (single-end or paired-end).
  • Reference FASTA, pre-indexed for BWA-MEM2.
• Optional:
  • Read group string (@RG\tID:...\tSM:...\tPL:...\tLB:...\tPU:...).
  • Number of threads (default: 4).
  • Output directory (default: current directory).
  • Temporary directory for sorting/dedup intermediates.
  • Optical duplicate pixel distance (default: 2500 for patterned flowcells).
  • Mark-duplicate tool choice: picard (default) or samtools markdup.

Workflow

1. Validate that reference index files exist (.0123, .amb, .ann, .bwt.2bit.64, .pac, .fai, .dict).
2. Construct a read group string from sample metadata if one is not provided (fields: ID, SM, PL, LB, PU).
3. Run bwa-mem2 mem with the read group, piping output to samtools sort to produce a coordinate-sorted BAM.
4. Index the sorted BAM with samtools index.
5. Mark duplicates with picard MarkDuplicates (or samtools markdup if selected).
6. Index the deduplicated BAM.
7. Report alignment summary: total reads, mapped reads, properly paired reads, duplicate reads, mapping rate.

Output Contract

• Coordinate-sorted deduplicated BAM file (.bam).
• BAM index file (.bai).
• Duplicate metrics file (picard MarkDuplicates output).
• Alignment summary statistics (total, mapped, properly paired, duplicates, mapping rate).

Limits

• BWA-MEM2, samtools, and picard must be installed and available on $PATH.
• The BWA-MEM2 index must be pre-built (bwa-mem2 index <ref.fa>).
• Memory scales with reference genome size (~8 GB for human GRCh38).
• Picard requires a Java runtime (Java 8+).
• This skill handles single-sample alignment only; multi-sample merging is out of scope.
• Common failure cases:
  • Reference index files missing or incomplete (e.g., .bwt.2bit.64 absent).
  • Read group string malformed or missing required fields (ID, SM).
  • Insufficient memory for BWA-MEM2 index loading (~8 GB for human genome).