---
name: "unknown"
section: "1"
platform: "linux"
package: "fastlink"
version: "4.1P-fix100+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/unknown"
---

# unknown(1)

identify possible genotypes for unknowns

## NAME

unknown - identify possible genotypes for unknowns

## SYNOPSIS

A program to rapidly identify which genotypes are possible for individuals typed as unknowns in the input pedigree.

**unknown** \[ **-cl** \]

## DESCRIPTION

**unknown** infers possible genotypes and mating combinations for parents with unknown genotypes for  [*ilink*(1)](/ilink/1.md), [*mlink*(1)](/mlink/1.md) and [*linkmap*(1)](/linkmap/1.md).

## OPTIONS

- **-c**

  Use conditional allele frequencies.

- **-l**

  Choose a good set of loop breakers automatically.

## RETURN VALUE

0	Successful completion

## ERRORS

```
10	File not found
255	Failure
```

## EXAMPLES

Normally, [**unknown**(1)](/unknown/1.md) is run immediately prior to its sister programs, [*ilink*(1)](/ilink/1.md), [*mlink*(1)](/mlink/1.md) and [*linkmap*(1)](/linkmap/1.md), like this:

unknown\
 mlink

## FILES

[**unknown**(1)](/unknown/1.md) reads the two files *pedfile.dat* and *datafile.dat* as its own input and produces various temporary files that are used as input to the next program. These temporary files are *ipedfile.dat*, *upedfile.dat*, *speedfile.dat* and *newspeedfile.dat*.

## NOTES

[**unknown**(1)](/unknown/1.md) is part of the **FASTLINK** package, which is a re-implementation of the **LINKAGE** suite of computer tools that help investigate genetic linkage as first proposed G.M. Lathrop, J.M. Lalouel, C. Julier, and J. Ott.

## AUTHORS

Dylan Cooper, Alejandro Schaffer, and Tony Schurtz based on work originally by Jurg Ott, Ph.D, et. al.

This manual page was written by  Elizabeth Barham \<lizzy@soggytrousers.net\> for the Debian GNU/Linux system (but may be used by others).

## WORD-WIDE-WEB

http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html

## SEE ALSO

[*ilink*(1)](/ilink/1.md), [*linkmap*(1)](/linkmap/1.md), [*lodscore*(1)](/lodscore/1.md), [*mlink*(1)](/mlink/1.md).