karyo_RxRy

Script for karyotypic sex inference and detection of autosomal and sex chromosomal aneuploidies using ancient DNA.
The script is an update to Skoglund et al. 2013 (https://github.com/pontussk/ry_compute), identifying individuals with possible sex karyotypes: 46XX, 46XY, 47XXX, 47XXY, 47XYY, 45X0, as well as additional copies of chromosome 21.
Recommended input -> BAM files.

Usage

Whole genome sequencing data

For shotgun sequencing data, we recommend using the default version of the script on filtered BAM files with MAPQ > 30.

Example using shotgun sequencing data

samtools view -q 30 bamfile.bam | python2 karyo_RxRy.py

Target enrichment data

For genome-wide data sequenced after target enrichment with the "1240k" array, we recommend using the --capture option.

Example using target enrichment data

samtools view -q 30 bamfile.bam | python2 karyo_RxRy.py --capture

Chromosome 21

Using the option --chr21, the output will include 2 additional columns for the R21 estimate and the Standard Error.
Estimates higher than 0.02 indicate the presence of an additional copy of chromosome 21 and therefore a karyotype of 47X*,+21.

Example command to output R21

samtools view -q 30 bamfile.bam | python2 karyo_RxRy.py --chr21

Example output

Na	Rx	RxSE	Ry	RySE	Assignment
17243391	0.0297	4.088e-05	0.0024	1.1915e-05	XY

• Na: Number of sequences mapping to autosomes (excluding chromosomes 13, 18, and 21)
• Rx: Number of sequences mapping to chromosome X over Na
• RxSE: Standard Error for Rx
• Ry: Number of sequences mapping to chromosome Y over Na
• RySE: Standard Error for Ry
• Assignment: Identified karyotype with possible values:
  • XX
  • XY
  • XXX
  • XXY
  • XYY
  • X0
  • Contamination
  • Consistent_with_XX
  • Consistent_with_XY

Output header can be removed using --noheader.

Citation

Anastasiadou, K. et al. (2023). Detection of chromosomal aneuploidy in ancient genomes. Communications Biology. 10.1038/s42003-023-05642-z.

Contacts

kyriaki.anastasiadou@crick.ac.uk
pontus.skoglund@gmail.com