Monthly Archives: October 2016

I have added the likelihood ratio test (LRT) for logistic regression into seer, in addition to the existing Wald test as noted in issue 42. As this is likely to remain undocumented elsewhere, here are some brief notes:

  • Both the p-value from the Wald test, and the p-value from the new LRT are in the output.
  • The LRT is expected to be a more powerful test in some situations. I would recommend its use over the Wald test.
  • Testing has shown some clear cases (e.g. when population structure is not a major effect) where the Wald test performs poorly, and the LRT recovers the power of a chi-squared test.
  • I have also put in a LRT for linear regression, but based on an estimate of the residual errors (which therefore gives slightly different results to R at small sample sizes). I don’t expect it to make much, if any, difference in this case.

There’s a nice article on the Wald, LRT and score tests here.

I’ll package this update in a future release, but if you want it now you can checkout the master branch and compile it yourself.

I want to count the number of unique patterns in a vcf file. First I convert it to text with bcftools query:

bcftools query -f '[%GT]\n' vcf_in.vcf.gz > patterns.txt

The resulting patterns.txt is about 100Gb. The best way I found to count the unique patterns in this was with the following command:

LC_ALL=C sort -u --parallel=4 -S 990M -T ~/tmp_sort_files patterns.txt | wc -l

This used 1063Mb RAM, took 1521s and used a maximum of around 75Gb tmp space on my home (as the /tmp drive on the cluster ran out of space).

With thanks to

I was working on an OS X system which kept getting annoying pop-ups about the system needing clean up, anti-virus software etc. I was able to see that the window was titled ‘helperamc’.

It turns out this was a remnant from Advanced Mac Cleaner, the use of which I won’t comment on here. The user of the system had tried to remove it when upgrading OS X version, but the annoying advertising component remained.

Killing the process and deleting the application doesn’t work, as it has a daemon to relaunch itself. After some investigation I found the following commands (issued in will sort out this issue and remove helperamc for good:

launchctl unload ~/Library/LaunchAgents/com.pcv.hlpramcn.plist
rm ~/Library/Application\ Support/amc/

As they are user files admin access is not needed. You may need to kill the helperamc process between these commands.