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# Undocumented change in 2.4? (-A DepthOfCoverage)

Sanger, Cambridge, UKPosts: 63Member
edited March 2013

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)

Post edited by TechnicalVault on

Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute

Tagged:

• Sanger, Cambridge, UKPosts: 63Member

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?

Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute

• Posts: 61Member

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

Geraldine Van der Auwera, PhD

• Posts: 61Member
edited May 2013

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

QD QualByDepth

MQRankSum MappingQualityRankSumTest

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:

Thanks.

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

Post edited by tommycarstensen on

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...

Geraldine Van der Auwera, PhD

• Sanger, Cambridge, UKPosts: 63Member

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].

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

Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute

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.

Geraldine Van der Auwera, PhD

• Sanger, Cambridge, UKPosts: 63Member

Just tried that on GATK 2.5-2 and got:

java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations
INFO  15:54:36,033 HelpFormatter - ------------------------------------------------------------
INFO  15:54:36,035 HelpFormatter - Program Name: org.broadinstitute.sting.tools.ListAnnotations
INFO  15:54:36,038 HelpFormatter - Program Args:
INFO  15:54:36,039 HelpFormatter - Date/Time: 2013/05/22 15:54:36
INFO  15:54:36,039 HelpFormatter - ------------------------------------------------------------
INFO  15:54:36,039 HelpFormatter - ------------------------------------------------------------
at java.net.URLClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
... 4 more


Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute

• Sanger, Cambridge, UKPosts: 63Member

On latest nightly I get the following error message (but this may just be because it's a nightly:

java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations
at java.net.URLClassLoader.access$000(Unknown Source) at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)