RAREMETAL is a program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.

Reference:

• Feng, Shuang, et al. "RAREMETAL: fast and powerful meta-analysis for rare variants." Bioinformatics 30.19 (2014): 2828-2829.

• RAREMETAL Main Site
• RAREMETAL GitHub repository

• Module Name: raremetal (see the modules page for more information)
• Environment variables set
  • RAREMETAL_HOME

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive --cpus-per-task=4 --mem=8G --gres=lscratch:10
salloc.exe: Pending job allocation 42848391
salloc.exe: job 42848391 queued and waiting for resources
salloc.exe: job 42848391 has been allocated resources
salloc.exe: Granted job allocation 42848391
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3101 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@cn3101 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3101 42848391]$ cp -r /fdb/raremetal/4.15.1/raremetal_tutorial .

[user@cn3101 42848391]$ cd raremetal_tutorial/

[user@cn3101 raremetal_tutorial]$ module load raremetal samtools
[+] Loading raremetal  4.15.1  on cn3101
[+] Loading singularity  3.4.2  on cn3101
[+] Loading samtools 1.9  ...

[user@cn3101 raremetal_tutorial]$ raremetalworker  --ped example1.ped --dat example1.dat --vcf example1.vcf.gz \
     --traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno \
     --prefix STUDY1

RAREMETALWORKER 4.15.1 -- A Forerunner of RareMetal
          (c) 2012-2016 Shuang Feng, Dajiang Liu, Sai Chen, Goncalo Abecasis
[...snip...]

[user@cn3101 raremetal_tutorial]$ raremetalworker  --ped example2.ped --dat example2.dat --vcf example2.vcf.gz \
     --traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno \
     --prefix STUDY2

RAREMETALWORKER 4.15.1 -- A Forerunner of RareMetal
          (c) 2012-2016 Shuang Feng, Dajiang Liu, Sai Chen, Goncalo Abecass
[...snip...]

[user@cn3101 raremetal_tutorial]$ bgzip STUDY1.QT1.singlevar.score.txt

[user@cn3101 raremetal_tutorial]$ tabix -c "#" -s 1 -b 2 -e 2 STUDY1.QT1.singlevar.score.txt.gz

[user@cn3101 raremetal_tutorial]$ bgzip STUDY1.QT1.singlevar.cov.txt

[user@cn3101 raremetal_tutorial]$ tabix -c "#" -s 1 -b 2 -e 2 STUDY1.QT1.singlevar.cov.txt.gz

[user@cn3101 raremetal_tutorial]$ bgzip STUDY2.QT1.singlevar.score.txt

[user@cn3101 raremetal_tutorial]$ tabix -c "#" -s 1 -b 2 -e 2 STUDY2.QT1.singlevar.score.txt.gz

[user@cn3101 raremetal_tutorial]$ bgzip STUDY2.QT1.singlevar.cov.txt

[user@cn3101 raremetal_tutorial]$ tabix -c "#" -s 1 -b 2 -e 2 STUDY2.QT1.singlevar.cov.txt.gz

[user@cn3101 raremetal_tutorial]$ cat >summaryfiles<<"EOF"
STUDY1.QT1.singlevar.score.txt.gz
STUDY2.QT1.singlevar.score.txt.gz
EOF

[user@cn3101 raremetal_tutorial]$ cat >covfiles<<"EOF"
STUDY1.QT1.singlevar.cov.txt.gz
STUDY2.QT1.singlevar.cov.txt.gz
EOF

[user@cn3101 raremetal_tutorial]$ raremetal --summaryFiles summaryfiles --covFiles covfiles \
    --groupFile group.file --SKAT --burden --MB --VT --longOutput \
    --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 --hwe 1.0e-05 \
    --callRate 0.95 -

RAREMETAL 4.15.1 -- A Tool for Rare Variants Meta-Analyses for Quantitative Traits
          (c) 2012-2017 Shuang Feng, Dajiang Liu, Sai Chen, Goncalo Abecasis

[...snip...]

[user@cn3101 raremetal_tutorial]$ ls
COMBINED.QT1.meta.burden.results      example2.vcf.gz
COMBINED.QT1.meta.MB.results          example2.vcf.gz.tbi
COMBINED.QT1.meta.plots.pdf           group.file
COMBINED.QT1.meta.singlevar.results   STUDY1.Empirical.Kinship.gz
COMBINED.QT1.meta.SKAT_.results       STUDY1.QT1.additive.plots.pdf
COMBINED.QT1.meta.tophits.burden.tbl  STUDY1.QT1.singlevar.cov.txt.gz
COMBINED.QT1.meta.tophits.MB.tbl      STUDY1.QT1.singlevar.cov.txt.gz.tbi
COMBINED.QT1.meta.tophits.SKAT.tbl    STUDY1.QT1.singlevar.score.txt.gz
COMBINED.QT1.meta.tophits.VT.tbl      STUDY1.QT1.singlevar.score.txt.gz.tbi
COMBINED.QT1.meta.VT_.results         STUDY1.singlevar.log
COMBINED.QT1.raremetal.log            STUDY2.Empirical.Kinship.gz
command_to_use                        STUDY2.QT1.additive.plots.pdf
covfiles                              STUDY2.QT1.singlevar.cov.txt.gz
example1.dat                          STUDY2.QT1.singlevar.cov.txt.gz.tbi
example1.ped                          STUDY2.QT1.singlevar.score.txt.gz
example1.vcf.gz                       STUDY2.QT1.singlevar.score.txt.gz.tbi
example1.vcf.gz.tbi                   STUDY2.singlevar.log
example2.dat                          summaryfiles
example2.ped

[user@cn3101 raremetal_tutorial]$ exit
exit
salloc.exe: Relinquishing job allocation 42848391

[user@biowulf ~]$

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

#!/bin/bash
set -e
module load raremetal
raremetal --summaryFiles summaryfiles --covFiles covfiles \
    --groupFile group.file --SKAT --burden --MB --VT --longOutput \
    --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 --hwe 1.0e-05 \
    --callRate 0.95 -

Submit this job using the Slurm sbatch command.

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

Create a swarmfile (e.g. raremetal.swarm). For example:

raremetal --summaryFiles summaryfiles --covFiles covfiles \
    --groupFile group.file --SKAT --burden --MB --VT --longOutput \
    --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 --hwe 1.0e-05 \
    --callRate 0.95 -
raremetal --summaryFiles summaryfiles --covFiles covfiles \
    --groupFile group.file --SKAT --burden --MB --VT --longOutput \
    --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT2 --hwe 1.0e-05 \
    --callRate 0.95 -
raremetal --summaryFiles summaryfiles --covFiles covfiles \
    --groupFile group.file --SKAT --burden --MB --VT --longOutput \
    --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT3 --hwe 1.0e-05 \
    --callRate 0.95 -

Submit this job using the swarm command.

swarm -f raremetal.swarm [-g #] [-t #] --module raremetal