VITESSE - Handout from 10/18/2000 course
This file briefly describes the similarities and differences in
using VITESSE compared with LINKAGE/FASTLINK.
- The LINKAGE utilities preplink, makeped, lsp, lrp are used in
the same way.
- The output contains similar information and is
printed both to the screen and to files.
- VITESSE provides the functionality of both MLINK and LINKMAP
with one program.
- The LINKAGE/FASTLINK pre-processor program UNKNOWN is not used.
- The scripts produced by lcp must be passed through a filter called
cnvrt_sh to make them suitable for VITESSE.
- The output contains a lot of diagnostic information about how the
computation is proceeding. This diagnostic information is
helpful only if you read the paper about VITESSE.
- VITESSE computes exact likelihoods, while LINKAGE/FASTLINK compute
scaled likelihoods that are multiplied by a number that depends on the
pedigree structure. The effect of the scaling is eliminated when
one takes the difference of two log(likelihood) terms as is done
in computing a lodscore.
- The standard output file names are:
Here are some brief examples of how to run VITESSE.
We start with shell scripts for MLINK and LINKMAP as produced
by lcp (see the instructions for lcp). Then run:
Input file :mlink-pedin
Output file: vmlink-pedin
-> 88 lines processed
Input file :linkmap-pedin
Output file: vlinkmap-pedin
-> 155 lines processed
If VITESSE sees a complex (i.e., not simple) pedigree in the
input. It will abort. If you have a data set with multiple
pedigrees, some of which are not simple, my advice is:
- Use FASTLINK MLINK
- Use a combination of FASTLINK LINKMAP for the complex pedigrees and
VITESSE for the simple pedigrees. Then use
Jim Tomlin's (email@example.com) FASTESSE perl program
to automagically merge the FASTLINK and VITESSE results.