Description

Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

4 ()

5 ()

6 ()

7 ()

min_prob (float)

Minimum posterior probability P(G|R) in validation data

min_dp (integer)

Minimum coverage in validation data. If FORMAT/DP is missing and --minDP > 0, the program exits with an error.

bins (string)

Allele frequency bins used for rsquared computations. By default they should as MAF bins [0-0.5], while they should take the full range [0-1] if --use-ref-alt is used.

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

glimpse Documentation

GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.

https://github.com/odelaneau/GLIMPSEdoi: 10.1038/s41588-020-00756-0License: MIT
Authors