HPC – Lampredi – software update – Polymutt 0.15

$ ls -l $POLYMUTTDIR
total 12
drwxr-xr-x 2 root root 4096 Oct 28 14:47 bin
drwxr-xr-x 2 root root 4096 Oct 28 14:47 doc
drwxr-xr-x 2 root root 4096 Oct 28 14:47 example

$ polymutt --help

The following parameters are in effect:
pedfile : (-pname)
datfile : (-dname)
glfIndexFile : (-gname)
posterior cutoff : 0.50 (-c99.999)

Additional Options
Alternative input file : --in_vcf [], --mixed_vcf_records
Scaled mutation rate : --theta [1.0e-03], --indel_theta [1.0e-04]
Prior of ts/tv ratio : --poly_tstv [2.00]
Non-autosome labels : --chrX [X], --chrY [Y], --MT [MT]
de novo mutation : --denovo, --rate_denovo [1.5e-08],
[snip]

[...@node06(lampredi) ~]$ $POLYMUTTEXAMPLE/run.sh

The following parameters are in effect:
pedfile : test.ped (-pname)
datfile : test.dat (-dname)
glfIndexFile : test.gif (-gname)
posterior cutoff : 0.90 (-c99.999)
[snip]
Analysis started on Mon Oct 28 14:58:35 2013

Summary of reference -- 1
Total Entry Count: 81016
Total Base Cout: 81016
Non-Polymorphic Count: 72880
Transition Count: 5373
Transversion Count: 2763
Other Polymorphism Count: 0
Filter counts:
minMapQual 0
minTotalDepth 0
maxTotalDepth 0
Hard to call: 0
Skipped bases: 0
Analysis ended on Mon Oct 28 14:58:42 2013

Running time is 7 seconds
[snip]

Title: Polymutt
Summary: Calls single nucleotide variants and detects de novo point mutation events in families for next-generation sequencing data
License: NONFREE - modification granted; distribution of modifications prohibited
Group: Bioinformatics
URL: http://genome.sph.umich.edu/wiki/Polymutt

Name: polymutt
Version: 0.15
Module: apps/polymutt/0.15/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/polymutt/0.15/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/polymutt/0.15/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@ea64008
Package: apps/polymutt/0.15@b8b7f565
Last update: 2013-10-28

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-28T14:47:12
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

----------- Module Specific Help for 'apps/polymutt/0.15/gcc-4.4.6' ---------------------------

======== Polymutt ========
Calls single nucleotide variants and detects de novo point
mutation events in families for next-generation sequencing
data
=========================

This module sets up your environment for the use of the 'polymutt'
application. This module sets up version '0.15' of the
application.

>> SYNOPSIS <> LICENSING <> FURTHER INFORMATION <> GET STARTED <<

/opt/gridware/etc/modules/apps/polymutt/0.15/gcc-4.4.6:

module-whatis

Title: Polymutt
Summary: Calls single nucleotide variants and detects de novo point mutation events in families for next-generation sequencing data
License: NONFREE - modification granted; distribution of modifications prohibited
Group: Bioinformatics
URL: http://genome.sph.umich.edu/wiki/Polymutt

Name: polymutt
Version: 0.15
Module: apps/polymutt/0.15/gcc-4.4.6
Module path: /opt/gridware/etc/modules/apps/polymutt/0.15/gcc-4.4.6
Package path: /opt/gridware/pkg/apps/polymutt/0.15/gcc-4.4.6

Repository: git+http://download.alces-software.com/git/packager-base@ea64008
Package: apps/polymutt/0.15@b8b7f565
Last update: 2013-10-28

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-10-28T14:47:12
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)

For further information, execute:

module help apps/polymutt/0.15/gcc-4.4.6