genomics-pipeline

Step 16: Coverage QC and Sex Chromosome Verification

What This Does

Ultra-fast whole-genome coverage profiling directly from the BAM index file. Infers sex chromosome copy number (CNchrX, CNchrY) and detects sex chromosome aneuploidies (XXY, XYY, X0). Produces per-chromosome depth uniformity plots.

Why

Coverage QC catches alignment problems, sample swaps, and sequencing artifacts early — before spending hours on variant calling. Sex chromosome verification confirms sample identity and can reveal clinically significant aneuploidies like Klinefelter syndrome (XXY).

Tool

• goleft indexcov (Brent Pedersen)

Docker Image

quay.io/biocontainers/goleft:0.2.4--h9ee0642_1

Command

mkdir -p ${GENOME_DIR}/${SAMPLE}/indexcov

docker run --rm \
  --cpus 2 --memory 4g \
  -v ${GENOME_DIR}:/genome \
  quay.io/biocontainers/goleft:0.2.4--h9ee0642_1 \
  goleft indexcov \
  --directory /genome/${SAMPLE}/indexcov \
  /genome/${SAMPLE}/aligned/${SAMPLE}_sorted.bam

Output Files

| File | Description | |—|—| | indexcov-indexcov.ped | PED file with CN values for chrX, chrY, and autosomes | | indexcov-indexcov.roc | ROC-like data for each chromosome | | indexcov-indexcov.bed.gz | Per-16KB-bin normalized depth across all chromosomes | | index.html | Interactive HTML report with all plots |

Interpretation

Sex Chromosome Copy Number

| Karyotype | CNchrX | CNchrY | Meaning | |—|—|—|—| | 46,XY (male) | ~1.0 | ~1.0 | Normal male | | 46,XX (female) | ~2.0 | ~0.0 | Normal female | | 47,XXY (Klinefelter) | ~2.0 | ~1.0 | Male with extra X | | 47,XYY | ~1.0 | ~2.0 | Male with extra Y | | 45,X (Turner) | ~1.0 | ~0.0 | Female with single X |

Coverage Uniformity

• Flat depth across a chromosome = good sequencing
• Dips or spikes = possible CNVs, GC bias, or capture artifacts
• Systematic deviations across all chromosomes = library prep or sequencing problems

Runtime

~5 seconds per sample.

Notes

• Should be run as an early QC step after alignment (step 2). It only reads the .bai index, not the full BAM.
• Requires the BAM index (.bai) to exist alongside the BAM file.
• Works on any number of samples simultaneously — useful for batch QC.
• The HTML report is self-contained and can be opened in any browser.
• For single-sample runs, the sex chromosome plot is still useful but the population-level clustering view is less informative.

This site is open source. Improve this page.