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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

[email protected]
[email protected]

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Script for sex identification and aneuploidy detection using ancient DNA.

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