METAL

GitHub: https://github.com/statgen/METAL

Installed modules

module avail metal
module load metal/2011-03-25
 

then which metal will point to /usr/local/Cluster-Apps/metal/2011-03-25/generic-metal/executables/metal.

It is clear that this is an older version.

Installing from source

We resort to an up-to-date version here – a notable feature is that the effect/standard error fields allow for more decimal places,

cd /rds/user/$USER/hpc-work
wget -qO- https://github.com/statgen/METAL/archive/2020-05-05.tar.gz | \
tar xvfz -
cd METAL-2020-05-05
mkdir build && cd build
cmake ..
make
make test
make install
ln -sf /rds/user/$USER/hpc-work/METAL-2020-05-05/build/bin/metal /rds/user/$USER/hpc-work/bin/metal
 

where the last command generates a symbolic link to the executable, so that metal is in the search path and can be called anywhere.

Adaptation

We have modified source code to encapsulate information for two extensions,

on more decimal places for effect sizes and standard errors.
on variant significant statistics such that the +/- signs in the direction field of METAL output becomes p/n when they also have p-value <= 0.05. This faciliates selection of variants using criteria such as flagging variants to be significant at least at the 0.05 level.

A version is available here, https://github.com/cambridge-ceu/METAL; see the release notes there for the changes made.

Examples

The tests/ directory contains 10 variations and can be run from the build/ directory as follows,

make test

which gives,

make test
Running tests...
Test project /home/jhz22/hpc-work/METAL-2020-05-05/build
      Start  1: NORMP
 1/12 Test  #1: NORMP ...................................   Passed    0.10 sec
      Start  2: BINORMP
 2/12 Test  #2: BINORMP .................................   Passed    0.05 sec
      Start  3: BINORMQ
 3/12 Test  #3: BINORMQ .................................   Passed    0.01 sec
      Start  4: SAMPLESIZE_NOGC
 4/12 Test  #4: SAMPLESIZE_NOGC .........................   Passed    0.70 sec
      Start  5: SAMPLESIZE_GC
 5/12 Test  #5: SAMPLESIZE_GC ...........................   Passed    0.24 sec
      Start  6: STDERR_NOGC
 6/12 Test  #6: STDERR_NOGC .............................   Passed    0.26 sec
      Start  7: STDERR_GC
 7/12 Test  #7: STDERR_GC ...............................   Passed    0.23 sec
      Start  8: SAMPLESIZE_NOGC_HETEROGENEITY
 8/12 Test  #8: SAMPLESIZE_NOGC_HETEROGENEITY ...........   Passed    0.41 sec
      Start  9: STDERR_NOGC_HETEROGENEITY
 9/12 Test  #9: STDERR_NOGC_HETEROGENEITY ...............   Passed    0.29 sec
      Start 10: SAMPLESIZE_NOGC_OVERLAP_HETEROGENEITY
10/12 Test #10: SAMPLESIZE_NOGC_OVERLAP_HETEROGENEITY ...   Passed    0.38 sec
      Start 11: TRACK_POSITIONS
11/12 Test #11: TRACK_POSITIONS .........................   Passed    0.26 sec
      Start 12: PRINT_PRECISION
12/12 Test #12: PRINT_PRECISION .........................   Passed    0.25 sec

100% tests passed, 0 tests failed out of 12

Total Test time (real) =   3.53 sec
 