Undocumented change in 2.4? (-A DepthOfCoverage)

TechnicalVault

Just in the process of updating our pipeline from v2.3-4-gb8f1308 Lite to v2.4-7-g5e89f01 Academic and have run into a small issue. The command line:

-T UnifiedGenotyper -glm SNP -R /lustre/scratch111/resources/ref/Homo_sapiens/1000Genomes_hs37d5/hs37d5.fa -I /lustre/scratch111/projects/helic/vcf-newpipe/lists/chr1-pooled.list --alleles /lustre/scratch111/projects/helic/vcf-newpipe/pooled/1/1:1-1000000.snps.vcf.gz -L 1:1-1000000 -U LENIENT_VCF_PROCESSING -baq CALCULATE_AS_NECESSARY -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES --standard_min_confidence_threshold_for_calling 4.0 --standard_min_confidence_threshold_for_emitting 4.0 -l INFO -A QualByDepth -A HaplotypeScore -A MappingQualityRankSumTest -A ReadPosRankSumTest -A FisherStrand -A InbreedingCoeff -A DepthOfCoverage -o /lustre/scratch111/projects/helic/vcf-newpipe/pooled/1/1:1-1000000.asnps.vcf.gz.part.vcf.gz

This worked in 2.3.4. But now gives:

Invalid command line: Argument annotation has a bad value: Class DepthOfCoverage is not found; please check that you have specified the class name correctly

I've looked at the release notes but it's not giving me a clue as to what has changed. Has the DepthOfCoverage annotation now been dropped? I've checked and I can reproduce this on the latest nightly (nightly-2013-03-11-g184e5ac)

Geraldine_VdAuwera

Ah, sorry about that -- forgot to document it in the release notes. The DepthOfCoverage annotation has been renamed to Coverage, because of a naming conflict with the DepthOfCoverage walker.

Re: running VA --list without a full command-line, the official answer is that it's not a priority, but I'll see if I can do something about that.

TechnicalVault

Just been looking through VariantAnnotator --list and noticed there is now -A Coverage. I assume this is -A DepthOfCoverage renamed? Could this be added to the release notes please?

P.S. Small wishlist feature request, could you please make it possible to run VariantAnnotator --list without providing a -R reference and -V variants?

tommycarstensen

This page does not yet mention that DepthOfCoverage is obsolete in 2.4: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthOfCoverage.html

Geraldine_VdAuwera

Ah, thanks for pointing that out, Tommy. I'll fix that ASAP.

tommycarstensen

@TechnicalVault I've had some problems with VA 2.4 myself. I have created this list of annotation equivalents:

QD QualByDepth

MQRankSum MappingQualityRankSumTest

ReadPosRankSum ReadPosRankSumTest

MQ RMSMappingQuality

FS FisherStrand

DP Coverage (previously DepthOfCoverage)

These pages currently do not reflect the annotation changes, but it's an impossible task to update all of them:

http://www.broadinstitute.org/gatk/guide/article?id=1268

http://www.broadinstitute.org/gatk/guide/article?id=1259

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_VariantRecalibrator.html

http://gatkforums.broadinstitute.org/discussion/39/variant-quality-score-recalibration-vqsr

Thanks.

P.S. @Geraldine_VdAuwera I have the same feature as Martin on my wishlist (VA --list without full command line)

Geraldine_VdAuwera

Thanks Tommy, I fixed the mentions of Coverage in those docs. No task is impossible -- but it sure helps to have someone point these out! FYI, I also put in a symlink so that if anyone use the old DepthOfCoverage annotator doc link, they will be redirected to the appropriate Coverage page.

I'm looking into a solution for the VA --list issue. I tinkered with making a separate listing tool but the call is awkwardly long:

java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations

Comments welcome, but I'm guessing that's not really going to make anyone happy. It's difficult to make this a priority though, because the annotations are all listed in the online docs, so it's not like there's no way to find them. But I understand sometimes you just want to get a quick list from command line. So, stay tuned...

TechnicalVault

In the release notes for 2.5 it lists under variant annotator is has listed: "Can now use the --list option without needing a full valid command-line." [1] However as of 2.5-2 it still doesn't seem to work so I'm not quite sure what was changed [2].

[1] http://gatkforums.broadinstitute.org/discussion/2572/release-notes-for-gatk-version-2-5#latest

[2] test command line: java -jar GenomeAnalysisTK.jar -T VariantAnnotator --list

Geraldine_VdAuwera

Ah, I think that was an error we made in compiling the release notes. There is now a way to list annotations, but the command line is

java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations

which is admittedly a little awkward, so we're still looking into making --list work by itself.