Biowulf High Performance Computing at the NIH
Mendel: Exact Statistical Genetic Analysis of Qualitative and Quantitative Traits

Mendel is one of the few statistical genetics packages that provide a full spectrum of gene mapping methods, ranging from parametric linkage in large pedigrees to genome-wide association with rare variants. The latest additions to Mendel anticipate and respond to the needs of the genetics community. Compared with earlier versions, Mendel is faster and easier to use and has a wider range of applications.

References:

Documentation
Important Notes

Mendel software can be used to perform 31 different types of analysis:

1 MAPPING MARKERS             17 GENE DROPPING
2 LOCATION SCORES             18 COMBINING LOCI
3 PEDIGREE HAPLOTYPING        19 VARIANCE COMPONENTS
4 NPL                         20 QTL ASSOCIATION
5 MISTYPING                   21 TRIM PEDIGREES
6 ALLELE FREQUENCIES          22 ASSOCIATION GIVEN LINKAGE
7 RISK PREDICTION             23 SNP IMPUTATION
8 GAMETE COMPETITION          24 GWAS (SNP ASSOCIATION)
9 PEDIGREE SELECTION          25 FILE CONVERSION
10 KINSHIP                    26 MFG
11 GENETIC EQUILIBRIUM        27 INBRED STRAINS
12 ASSOCIATION BY PERMUTATION 28 SIMULATE TRAITS
13 TDT                        29 PED GWAS
14 PENETRANCES                30 QMFG LRT
15 ETHNIC ADMIXTURE           31 QMFG SCORE
16 COMBINING ALLELES
To perform a specific analysis, one needs to prepare the corresponding input data files, including the control, definition, map, pedigree and, in some cases, penetrance file, and then to pass the control file to the executable mendel with option -c. Examples of input files corresponding to different types of analysis can be found in $MENDEL_SAMPLE_INPUTS.
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load Mendel
We are going to focus on analysis of type 20 (QTL Association), so we first download the input data for this analysis.
[user@cn3144 ~]$ cp $MENDEL_SAMPLE_INPUTS/*20* . 
Now we run the analysis by passing one of the corresponding control files to the executable mendel:
[user@cn3144 ~]$ mendel -c Control20a.in 

                       WELCOME TO MENDEL, VERSION 16.0
 
                   (c) COPYRIGHT KENNETH LANGE, 1985-2016
                       ALL COMMERCIAL RIGHTS RESERVED
                   PROGRAMMED BY KENNETH LANGE & ERIC SOBEL
 
              DOCUMENTATION AND MOST RECENT VERSION AVAILABLE AT
                 http://www.genetics.ucla.edu/software/mendel

 
        READING AND INITIALIZING DATA ...
 
 INITIALIZATION RUN TIME  :  0.195 SECONDS

        MENDEL DATA INITIALIZATION COMPLETED.
 

        PERFORMING DATA ANALYSIS ...

 QTL ASSOCIATION OPTION
           1  -248.643608295694     
           2  -246.566607706464     
           3  -246.673547763017     
           4  -245.654820477465     
           5  -242.337916957557     
           6  -239.695884890016     
           7  -232.084217087074     
          ...
          19  -230.251687092604     
          20  -230.251686332244     
          21  -230.251686332085     
          22  -230.251686332083     
           1  -248.643608295694     
           2  -232.959594583250     
           3  -232.242654257396     
          ...
          13  -230.251686695477     
          14  -230.251686333397     
          15  -230.251686332261     

 WORKING ON LOCUS NUMBER:       1 (Gc).
  WORKING ON PERSON NUMBER            1  AT LOCUS NUMBER            1
  WORKING ON PERSON NUMBER            2  AT LOCUS NUMBER            1
  WORKING ON PERSON NUMBER            5  AT LOCUS NUMBER            1
  WORKING ON PERSON NUMBER            6  AT LOCUS NUMBER            1
  ...
  WORKING ON PERSON NUMBER          161  AT LOCUS NUMBER            1
  WORKING ON PERSON NUMBER          162  AT LOCUS NUMBER            1
  WORKING ON PERSON NUMBER          165  AT LOCUS NUMBER            1
  WORKING ON PERSON NUMBER          166  AT LOCUS NUMBER            1
  WORKING ON PERSON NUMBER          169  AT LOCUS NUMBER            1
  WORKING ON PERSON NUMBER          170  AT LOCUS NUMBER            1
  WORKING ON PERSON NUMBER          173  AT LOCUS NUMBER            1
  WORKING ON PERSON NUMBER          174  AT LOCUS NUMBER            1
           1  -230.251686332083     
           2  -223.290178747044     
           3  -219.485435067882     
           4  -219.146779791111     
           5  -218.857571119425     
           6  -218.644118846922     
           7  -218.224800510177     
           8  -217.975290979946     
           9  -217.848667861195     
          10  -217.828442118181     
          11  -217.827209876971     
          12  -217.825044759115     
          13  -217.825019940971     
          14  -217.825019470628     
          15  -217.825017863228     
          16  -217.825017066203     
 
 ANALYSIS RUN TIME  :  0.040 SECONDS

        MENDEL DATA ANALYSIS COMPLETED.
 
 
  THE FILE Summary20a.out CONTAINS THE SUMMARY OUTPUT.
  THE FILE Mendel20a.out CONTAINS THE DETAILED OUTPUT.
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. Mendel.sh). For example:

#!/bin/bash
module load Mendel    
mendel -c Control_file_1
mendel -c Control_file_2
...
mendel -c Control_file_N

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] Mendel.sh