Inferring the biological sex of ancient genomic shotgun samples
samtools view <MYBAM.bam> | python ry_compute.py [options]
Options: -h, --help show this help message and exit --chrXname=CHRXNAME Identifier for the X chromosome in the SAM input (use if different than chrX, X etc) --chrYname=CHRYNAME Identifier for the Y chromosome in the SAM input (use if different than chrY, Y etc) --malelimit=MALELIMIT Upper R_y limit for assignment as XY/male --femalelimit=FEMALELIMIT Lower R_y limit for assignment as XX/female --digits=DIGITS Number of decimal digits in R_y output --noheader Do not print header describing the columns in the output --idxstats Input is from samtools idxstats