GPTomics/bio-alignment-sorting

Version Compatibility

Reference examples tested with: pysam 0.22+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Alignment Sorting

Sort alignment files by coordinate or read name using samtools and pysam.

"Sort a BAM file" -> Reorder reads by genomic coordinate (for indexing/variant calling) or by name (for paired-end processing).

• CLI: samtools sort -o sorted.bam input.bam
• Python: pysam.sort('-o', 'sorted.bam', 'input.bam')

Sort Orders

| Order | Flag | Use Case | |-------|------|----------| | Coordinate | default | Indexing, visualization, variant calling | | Name | -n | Paired-end processing, fixmate, markdup | | Tag | -t TAG | Sort by specific tag value |

samtools sort

Sort by Coordinate (Default)

samtools sort -o sorted.bam input.bam

Sort by Read Name

samtools sort -n -o namesorted.bam input.bam

Multi-threaded Sorting

samtools sort -@ 8 -o sorted.bam input.bam

Control Memory Usage

samtools sort -m 4G -@ 4 -o sorted.bam input.bam

Set Temporary Directory

samtools sort -T /tmp/sort_tmp -o sorted.bam input.bam

Specify Output Format

# Output as BAM (default)
samtools sort -O bam -o sorted.bam input.bam

# Output as CRAM
samtools sort -O cram --reference ref.fa -o sorted.cram input.bam

Sort by Tag

# Sort by cell barcode (10x Genomics)
samtools sort -t CB -o sorted_by_barcode.bam input.bam

Pipe from Aligner

bwa mem ref.fa reads.fq | samtools sort -o aligned.bam

samtools collate vs sort -n

| Tool | Algorithm | Speed | Memory | Output guarantee | |------|-----------|-------|--------|------------------| | sort -n | Full lexicographic sort by QNAME | Slowest | Spills to -T | Strict total order by name | | collate | Hash-bucket grouping | ~3-10x faster | Bounded | Mates adjacent; between-mate order undefined |

Use collate when extracting paired FASTQ, re-aligning, or streaming through markdup. Use sort -n only when a tool requires true lexicographic name order (e.g. RSEM, Salmon alignment-mode).

# Fast paired FASTQ extraction
samtools collate -O -u in.bam tmp_prefix | \
    samtools fastq -1 R1.fq.gz -2 R2.fq.gz -0 /dev/null -s /dev/null -n -

# Markdup pre-processing (collate beats sort -n here)
samtools collate -O -u in.bam tmp_prefix | \
    samtools fixmate -m -u - - | \
    samtools sort -u - | \
    samtools markdup - out.bam

Sort Order Required by Downstream Tool

| Operation | Required sort | |-----------|---------------| | samtools index | coordinate (hard requirement) | | samtools fixmate -m | name (or collate; needs mates adjacent) | | samtools markdup | coordinate (after fixmate) | | GATK MarkDuplicatesSpark | coordinate or queryname | | samtools mpileup / bcftools mpileup | coordinate | | GATK HaplotypeCaller, Mutect2 | coordinate | | featureCounts / HTSeq | coordinate or name (-p for paired) | | umi_tools dedup | coordinate (with index) | | fgbio GroupReadsByUmi | any order accepted (template-coordinate recommended to avoid an internal re-sort) | | fgbio CallMolecularConsensusReads | grouped by MI tag (consumes GroupReadsByUmi output) | | Sniffles, cuteSV, Manta, Delly | coordinate (need SA tags) | | Salmon alignment-mode | name | | RSEM (with STAR --quantMode TranscriptomeSAM) | name (hard requirement) |

Check Sort Order

From Header

samtools view -H input.bam | grep "^@HD"
# SO:coordinate = coordinate sorted
# SO:queryname = name sorted
# SO:unsorted = not sorted

Verify Sorted

# Check if coordinate sorted (returns 0 if sorted). Reset the position tracker
# on each new contig, else the POS reset at every chromosome boundary of a
# correctly sorted multi-contig BAM would falsely report "unsorted".
samtools view input.bam | awk '$3!=c {c=$3; prev=0} $4<prev {exit 1} {prev=$4}'
# Simpler and authoritative: trust the @HD SO: header shown above.

pysam Python Alternative

Sort with pysam

import pysam

pysam.sort('-o', 'sorted.bam', 'input.bam')

Sort by Name

pysam.sort('-n', '-o', 'namesorted.bam', 'input.bam')

Sort with Options

pysam.sort('-@', '4', '-m', '2G', '-o', 'sorted.bam', 'input.bam')

Avoid In-Python Sorting

Do not load BAM records into a list and call sorted(). pysam.sort() calls samtools' external-merge sort which spills to disk; loading reads into memory blows up around ~30M reads (~10 GB human BAM). Always delegate to pysam.sort():

import pysam

pysam.sort('-@', '4', '-m', '2G', '-T', '/tmp/sortpfx',
           '-o', 'sorted.bam', 'input.bam')

Check Sort Order in pysam

import pysam

with pysam.AlignmentFile('input.bam', 'rb') as bam:
    hd = bam.header.get('HD', {})
    sort_order = hd.get('SO', 'unknown')
    print(f'Sort order: {sort_order}')

Stream Sort from Aligner

For streaming from aligners, use shell pipes (simpler and more reliable):

import subprocess

subprocess.run(
    'bwa mem ref.fa reads.fq | samtools sort -o aligned.bam',
    shell=True, check=True
)

samtools merge

Combine multiple BAM files into one. samtools merge does NOT validate sort-order consistency across inputs; mismatched inputs silently produce a malformed output.

Verify Sort Order Consistency First

for f in *.bam; do samtools view -H "$f" | head -1; done | sort -u
# Should print exactly ONE line, e.g. "@HD VN:1.6 SO:coordinate"

Safe Merge (dedup @RG and @PG)

# -c deduplicates @RG records; -p deduplicates @PG records (samtools-merge(1))
samtools merge -c -p -@ 8 merged.bam sample1.bam sample2.bam sample3.bam

When merging BAMs from different lanes / machines / aligners, RG IDs may collide. -c and -p deduplicate header records, but RG IDs that genuinely refer to different lane-level read groups must be made unique upstream (samtools addreplacerg) before merge -- otherwise GATK BQSR (which keys models by RGID/PU) silently produces wrong recalibration.

Merge with Threads / from File List

samtools merge -@ 4 merged.bam sample1.bam sample2.bam sample3.bam
samtools merge -b files.txt merged.bam   # one BAM path per line

Force Overwrite

samtools merge -f merged.bam sample1.bam sample2.bam

Merge Specific Region

samtools merge -R chr1:1000000-2000000 merged_region.bam sample1.bam sample2.bam

pysam Merge

import pysam

pysam.merge('-c', '-p', '-f', 'merged.bam', 'sample1.bam', 'sample2.bam', 'sample3.bam')

Common Workflows

Goal: Combine sorting with other alignment processing steps into efficient pipelines.

Approach: Pipe aligner output directly into samtools sort to avoid writing unsorted intermediates, then index for downstream access.

Align and Sort

bwa mem -t 8 ref.fa R1.fq R2.fq | samtools sort -@ 4 -o aligned.bam
samtools index aligned.bam

Re-sort by Name for Duplicate Marking

# Full workflow: sort by name, fixmate, sort by coord, markdup
samtools sort -n -o namesorted.bam input.bam
samtools fixmate -m namesorted.bam fixmate.bam
samtools sort -o sorted.bam fixmate.bam
samtools markdup sorted.bam marked.bam

Convert Name-sorted to Coordinate-sorted

samtools sort -o coord_sorted.bam name_sorted.bam
samtools index coord_sorted.bam

Extract FASTQ from Sorted BAM

# Collate first to group pairs
samtools collate -u -O input.bam /tmp/collate | \
    samtools fastq -1 R1.fq -2 R2.fq -0 /dev/null -s /dev/null -

Performance Tips

| Parameter | Effect | |-----------|--------| | -@ N | Use N additional threads | | -m SIZE | Memory per thread (e.g., 4G) | | -T PREFIX | Temp file location (use fast SSD scratch) | | -l LEVEL | Compression level (1-9, default 6) |

Compression Level Decision

| Level | Use | Wall-time vs default | Size vs default | |-------|-----|----------------------|------------------| | -l 0 / -u | Pipe between samtools tools | 0% (skips BGZF) | +200-400% | | -l 1 | Final output if disk is cheap | ~+10% | ~+30% | | -l 6 | Default | baseline | baseline | | -l 9 | Archival, write-once | ~+50-100% | ~-2-5% |

# WRONG -- pipe re-compresses then decompresses every step
samtools fixmate -m in.bam - | samtools sort -o out.bam

# RIGHT -- uncompressed (-u) between piped samtools commands
samtools fixmate -m -u in.bam - | samtools sort -o out.bam

Optimal Settings for Large Files

# 8 threads, 2GB per thread, low compression for output written to fast disk
samtools sort -@ 8 -m 2G -l 1 -T /scratch/sortpfx -o sorted.bam input.bam

Quick Reference

| Task | Command | |------|---------| | Sort by coordinate | samtools sort -o out.bam in.bam | | Sort by name | samtools sort -n -o out.bam in.bam | | Sort with threads | samtools sort -@ 8 -o out.bam in.bam | | Collate pairs | samtools collate -o out.bam in.bam | | Merge BAMs | samtools merge out.bam in1.bam in2.bam | | Check sort order | samtools view -H in.bam \| grep "^@HD" | | Sort + index | samtools sort -o out.bam in.bam && samtools index out.bam |

Common Errors

| Error | Cause | Solution | |-------|-------|----------| | out of memory | Insufficient RAM | Use -m to limit per-thread memory | | disk full | Temp files filling disk | Use -T to specify different location | | truncated file | Interrupted sort | Re-run sort from original |

Related Skills

• sam-bam-basics - View and convert alignment files
• alignment-indexing - Index after coordinate sorting
• duplicate-handling - Requires name-sorted input for fixmate
• alignment-filtering - Filter before or after sorting