As reported by Menachem Fromer: a critical bug in AFCalcResult:
Specifically, the implementation:
public boolean isPolymorphic(final Allele allele, final double log10minPNonRef) {
return getLog10PosteriorOfAFGt0ForAllele(allele) >= log10minPNonRef;
}
seems incorrect and should probably be:
getLog10PosteriorOfAFEq0ForAllele(allele) <= log10minPNonRef
The issue here is that the 30 represents a Phred-scaled probability of *error* and it's currently being compared to a log probability of *non-error*.
Instead, we need to require that our probability of error be less than the error threshold.
This bug has only a minor impact on the calls -- hardly any sites change -- which is good. But the inverted logic effects multi-allelic sites significantly. Basically you only hit this logic with multiple alleles, and in that case it'\s including extra alt alleles incorrectly, and throwing out good ones.
Change was to create a new function that properly handles thresholds that are PhredScaled quality scores:
/**
* Same as #isPolymorphic but takes a phred-scaled quality score as input
*/
public boolean isPolymorphicPhredScaledQual(final Allele allele, final double minPNonRefPhredScaledQual) {
if ( minPNonRefPhredScaledQual < 0 ) throw new IllegalArgumentException("phredScaledQual " + minPNonRefPhredScaledQual + " < 0 ");
final double log10Threshold = Math.log10(QualityUtils.qualToProb(minPNonRefPhredScaledQual));
return isPolymorphic(allele, log10Threshold);
}
numbers larger than 999 in the Errors column were printed out with commas (which looks like a separate column).
This wasn't caught earlier because there are no integration tests covering the csv. I'll add one into unstable in a sec.
Packaging from a non-clean working directory can result in an incorrect
jar. Now that we have external collaborators packaging and distributing
the GATK, not enforcing the clean requirement has become far too dangerous.
At the same time, invoking "clean" automatically through a direct
dependency would also be dangerous -- instead, it's better to error out
if a packaging target is invoked from a non-clean working dir.
The MD5s for these tests were changed in commit 87435f1074615b2cd016f042980109fd53962c8d
to match the output of a broken version of BaseRecalibration. With the patch in
commit c397102ecc1fd1d2cd8f209a8f358ab4a60b50a7, the output once again matches the
*original* MD5s for these tests, and does not vary as you increase -nct.
Final resolution to GSA-632
-- Providing this optional argument -maxRuntime (in -maxRuntimeUnits units) causes the GATK to exit gracefully when the max. runtime has been exceeded. By cleanly I mean that the engine simply stops at the next available cycle in the walker as through the end of processing had been reached. This means that all output files are closed properly, etc.
-- Emits an info message that looks like "INFO 10:36:52,723 MicroScheduler - Aborting execution (cleanly) because the runtime has exceeded the requested maximum 10.0000 s". Otherwise there's currently no way to differentiate a truly completed run from a timelimit exceeded run, which may be a useful thing for a future update
-- Resolves GSA-630 / GATK max runtime to deal with bad LSA calling?
-- Added new JIRA entry for Ami to restart chr1 macarthur with this argument set to -maxRuntime 1 -maxRuntimeUnits DAYS to see if we can do all of chr1 in one weekend.
-- NCT wasn't previously recognized by Queue as needing more processors per machine. This commit fixes this. Also a potential cause of poor GATKPerformanceOverTime, in that runs with -nct could flood a node and cause it to have hundreds of cores in contention.
Mark DePristo
Eric Banks
Ryan Poplin
David Roazen
Andrey Sivachenko
Yossi Farjoun