Table 1: Parameters of ancIBD HMM and default values.

All parameters that can be set in our implementation. The default values are chosen to work well (low FP, high power, little length bias and variation) for a broad range of WGS and 1240k aDNA data (see Supp. Tab. 1D and 1E).

Parameter	Value	Description [Unit]
HMM
ibd_in	1	Transition rate out of non-IBD state [per Morgan]
ibd_out	10	Transition rate out of IBD states [per Morgan]
ibd_jump	400	Transition rate between IBD states [per Morgan]
min_error	0.001	Cap Min. Probabilitiy of diploid genotype Error [rate]
p	Sample/1000G	Allele Frequencies (AF)
Post-Processing
cutoff_post	0.99	Minimum Posterior on IBD state for IBD segment call
min_cm	2	Minimum Length IBD segment to call [centimorgan]
snp_cm	220	Minimum SNP density in IBD [per centimorgan]
max_gap	0.0075	Maximum Gap to merge [Morgan]