Skip to main content

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
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us