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Table 1 Analysis of FranceGenRef data. \(\widehat{\mathrm{\varphi }}\) is the estimate of the two siblings’ unobserved kinship coefficient \(\mathrm{\varphi }\)

From: Moment estimators of relatedness from low-depth whole-genome sequencing data

  WGS data at 30–40× Down-sampled WGS data at ~ 2.5×
Gaston
Full GRM
NGS-
RelateV2
LowKi (Unadjusted)* LowKi BEAGLE
 + 
LowKi
BEAGLE + 
SEEKIN
NGS-
RelateV2‡
Sibling Pair 1 \(\widehat{\varphi }\) 0.258 0.268 0.122 0.278 0.265 0.268 0.256
  \(\widehat{\psi }\) 0.294 0.379 0.059 0.185 0.255 0.459
Sibling Pair 2 \(\widehat{\varphi }\) 0.216 0.228 0.100 0.223 0.225 0.226 0.216
\(\widehat{\psi }\) 0.196 0.270 0.035 0.115 0.166 0.367
M (number of variants) 1,009,181 1,009,181 949,075 949,075 1,009,181
Time 4 min 4 min 15 h** 15 h ** 6 h
  1. \(\widehat{\psi }\) is the estimate of the two siblings’ unobserved fraternity coefficient \(\psi\). (*) Unadjusted values from LowKi, similar to in Additional file 1: Fig. S2. (**) The time required for these estimators is almost entirely due to BEAGLE, both LowKi and SEEKIN require only a few minutes. (†) SEEKIN does not provide estimates of \(\psi\). (‡) NGSRelateV2 results on down-sampled data should be compared to results from the same software but applied to the original data that had not been down-sampled