---
name: "bp_composite_LD"
section: "1p"
platform: "linux"
package: "bioperl"
version: "1.7.2-3"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/bp_composite_LD"
---

# bp\_composite\_LD(1p)

## NAME

bp\_composite\_LD -i filename.prettybase.txt --sortbyld \> outfile

## SYNOPSIS

```
  bp_composite_LD -i filename.prettybase [-o out.LD] [-f prettybase/csv] [--sortbyld] [--noconvertindels]
```

### DESCRIPTION

This a script which allows an easy way to calculate composite LD.

### OPTIONS

\-i or --in     filename

\-f or --format genotype format (prettybase or CSV)

\--sortbyld     To see data sorted by LD instead of just all the \
                site1/site2 pair LD values.

\-o or --out    output filename, otherwise will print to STDOUT

\--noconvert    (applicable for prettybase format file only)\
                if specified will NOT attempt to convert indel\
                states to 'I' and delete states ('-') to 'D'.

\-h or --help   see this documentation

### AUTHOR Jason Stajich, Matthew Hahn

For more information contact:

Matthew Hahn, \<matthew.hahn-at-duke.edu\> Jason Stajich \<jason-at-bioperl-dot-org\>