bio-duplicate-handling

What this skill does

## Version Compatibility

Reference examples tested with: picard 3.1+, 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.

# Duplicate Handling

**"Remove PCR duplicates from my BAM file"** -> Mark or remove duplicate reads using the fixmate-sort-markdup pipeline to prevent duplicate bias in variant calling.
- CLI: `samtools fixmate`, `samtools markdup` (samtools)
- Python: `pysam.fixmate()`, `pysam.markdup()` (pysam)

Mark and remove PCR/optical duplicates using samtools.

## Why Remove Duplicates?

PCR duplicates are identical copies of the same original molecule, created during library preparation. They inflate coverage, bias allele frequencies, and create false positive variant calls. Optical duplicates are flowcell-proximity artifacts of bridge amplification (especially on patterned NovaSeq / NovaSeq X / NextSeq 1000 flowcells).

## When to Mark Duplicates -- and When NOT To

Standard `samtools markdup` is the right tool for some assays and actively harmful for others. The decision is assay-driven:

| Assay | Standard markdup? | Recommended approach |
|-------|------------------|----------------------|
| Germline WGS / WES (PCR or PCR-free) | YES | `samtools markdup` (PCR-free still has ~0.5% optical duplicates on patterned flowcells) |
| Somatic tumor/normal (no UMI) | YES | Same |
| Exome / target capture | YES (20-50% expected) | `samtools markdup` |
| ChIP-seq | **MARK, do not remove** | Then use peak caller's auto-dup logic (`macs3 --keep-dup auto`) |
| CUT&RUN / CUT&Tag | MARK, do not remove | Same |
| ATAC-seq | YES, BEFORE Tn5 +4/-5 shift | Then shift coords for footprinting |
| Bulk RNA-seq (no UMIs) | **NO** | Duplicates are biological at highly-expressed loci; removing them biases DE proportional to expression |
| Bulk RNA-seq (with UMIs) | NO | umi_tools dedup |
| scRNA (10x, STARsolo, drop-seq) | **NO** | umi_tools dedup with CB+UB tags, or rely on Cell Ranger UMI counts |
| ctDNA / liquid biopsy / deep panel (UMI) | NO | fgbio GroupReadsByUmi -> CallDuplexConsensusReads |
| Twist / IDT / Roche UMI capture | NO | fgbio or Picard UmiAwareMarkDuplicatesWithMateCigar |
| Amplicon / hotspot panel (no UMI) | **NO** | Every read is a "duplicate" by coordinate; markdup erases the dataset. Use `samtools ampliconclip` instead -- see alignment-amplicon-clipping. |
| Amplicon / hotspot panel (UMI) | NO | fgbio consensus |
| Long-read native (ONT, PacBio HiFi unamplified) | NO | No PCR step; markdup is meaningless |
| PacBio HiFi amplicon | YES (rare) | `pbmarkdup` |
| Ancient DNA (aDNA) | YES + mapDamage | Run markdup, then mapDamage `--rescale` before variant calling |
| Microbiome 16S/ITS | NO | Read counts encode community structure |

If the BAM came from 10x Cell Ranger / STARsolo and `samtools markdup` produces a 50-95% duplicate rate, it is the wrong tool, not a bug.

## Tool Selection: markdup vs Picard vs UMI-aware

| Tool | Speed | Threading | Optical | UMI | Notes |
|------|-------|-----------|---------|-----|-------|
| `samtools markdup` | Fast | Yes | Yes (`-d`) | Limited (`--barcode-tag` exact-match) | Modern production default (nf-core/sarek) |
| `picard MarkDuplicates` | Slow | No | Yes | UmiAware variant (BETA, transcriptome bug) | GATK Best Practices reference |
| `biobambam2 bammarkduplicates2` | Fastest | Yes | Yes | No | Sanger / 1KGP pipelines |
| `samblaster` | Streaming, fast | No | Optional | No | Pipe directly from aligner; no name sort |
| `sambamba markdup` | Fast | Yes | Yes | No | Less actively maintained |
| `fgbio GroupReadsByUmi` + `CallMolecularConsensusReads` | Fast | Yes | n/a | **Best UMI tool** | Graph-based; supports duplex |
| `umi_tools dedup` | Slow | No | n/a | Yes (mature) | Reference for scRNA / bulk UMI |
| `pbmarkdup` | Fast | Yes | n/a | n/a | PacBio HiFi amplicons only |

Picard `UmiAwareMarkDuplicatesWithMateCigar` is BETA and has known bugs on transcriptome-aligned BAMs (silently keeps duplicates). Avoid for RNA-seq UMIs.

## Optical Distance Is Platform-Specific

`samtools markdup` default is `-d 0`, meaning **optical-duplicate detection is disabled by default**. Set explicitly per platform:

| Platform | `-d` value | Rationale |
|----------|-----------|-----------|
| HiSeq 2000/2500 (random) | 100 | Picard historic default |
| HiSeq 3000/4000/X (patterned) | 2500 | Patterned tile size larger |
| NovaSeq 6000 (patterned) | 2500 | Same as HiSeq X |
| NovaSeq X (10B) | 2500 (some Illumina field guidance suggests up to 12000) | Larger tiles |
| NextSeq 1000/2000 (patterned) | 2500 | ExAmp duplicates span larger pixel distances |
| MiSeq, NextSeq 500/550 | 100 | Smaller / unpatterned |
| Element AVITI, MGI / DNBseq | Custom regex | Different read-name format -- supply via `--read-coords` |

```bash
samtools markdup -d 2500 -t -f stats.txt input.bam marked.bam

# Count optical (SQ) vs library/PCR (LB) duplicates
samtools view -f 1024 marked.bam | grep -o 'dt:Z:[A-Z][A-Z]' | sort | uniq -c
```

Setting `-d 2500` on a HiSeq run does no harm. Forgetting `-d 2500` on NovaSeq systematically under-marks optical duplicates and overestimates library complexity.

## Multi-Library Pooled Marking

Without `--use-read-groups`, multi-library BAMs systematically over-mark: independent molecules from different libraries with the same coordinates get wrongly flagged as PCR duplicates. With `--use-read-groups`, RG tags must also match for two reads to be a duplicate (verify availability with `samtools markdup --help`):
```bash
samtools markdup --use-read-groups -d 2500 -t in.bam out.bam
```

samtools `--use-read-groups` keys on RG ID; Picard's library-aware behavior keys on the LB tag (allowing dedup across multiple lanes of the same library). For multi-lane single-library BAMs, Picard MarkDuplicates with `READ_NAME_REGEX` is closer to canonical.

## Duplicate Marking Workflow

**Goal:** Mark PCR/optical duplicates so they can be excluded from downstream variant calling and coverage analysis.

**Approach:** Name-sort, add mate tags with fixmate, coordinate-sort, then run markdup. The pipeline version avoids intermediate files.

**Reference (samtools 1.19+):**
```bash
# 1. Sort by name (required for fixmate)
samtools sort -n -o namesort.bam input.bam

# 2. Add mate information with fixmate
samtools fixmate -m namesort.bam fixmate.bam

# 3. Sort by coordinate (required for markdup)
samtools sort -o coordsort.bam fixmate.bam

# 4. Mark duplicates
samtools markdup coordsort.bam marked.bam

# 5. Index result
samtools index marked.bam
```

### Pipeline Version (Optimized)
```bash
# collate is faster than sort -n; -u/-O between piped tools skips BGZF round-trips
samtools collate -O -u input.bam tmpdir/collate | \
    samtools fixmate -m -u - - | \
    samtools sort -u -@ 4 -T tmpdir/sort - | \
    samtools markdup -@ 4 -d 2500 -t --use-read-groups \
        -f markdup_stats.txt - marked.bam

samtools index marked.bam
```

This is ~30% faster than `sort -n | fixmate | sort | markdup` on typical 30x WGS.

**Critical pitfall:** `samtools markdup` requires `ms` (mate score, lowercase) and `MC` (mate CIGAR) tags from `fixmate -m`. A re-sort that loses aux tags via Python round-trip silently produces a markdup output that marks almost nothing. If duplicate counts look implausibly low, verify `MC:Z:` is present in the input to markdup.

## samtools fixmate

Adds mate information required by markdup. Must be run on name-sorted BAM.

### Basic Usage
```bash
samtools fixmate namesorted.bam fixmate.bam
```

### Add Mate Score Tag (-m)
```bash
# Required for markdup to work correctly
samtools fixmate -m namesorted.bam fixmate.bam
```

### Multi-threaded
```bash
samtools fix