crukci-bioinformatics / gatk-tools Goto Github PK

Hi Matt,

Sorry for coming back with an issue again. It's likely me doing something wrong - I'm not very familiar with GATK. I'm getting an error when running run-gatk after building:

./gatk-tools-1.0-SNAPSHOT/bin/run-gatk -T ReadCountWalker

Giving me:

##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: ReadCountWalker

I followed the installation steps, including installing the GATK jar file using maven, and setting the CLASSPATH_PREFIX variable (without it set correctly, it gives another kind of error, so I think I didn't screw this up). However both the manually built version gatk-tools-1.0-SNAPSHOT and downloaded release gatk-tools-0.2.2 are giving same error about the missing ReadCountWalker. Can you suggest please?

Vlad

Hi Matt,

When I run mvn package, I'm getting BUILD FAILURE right after the attempt to download
gatk-3.7.pom:

[~/git/gatk-tools]$ mvn package
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building GATK Tools 1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading from bioinformatics: http://internal-bioinformatics.cruk.cam.ac.uk/maven/org/broadinstitute/gatk/gatk/3.7/gatk-3.7.pom
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.723 s
[INFO] Finished at: 2017-10-27T15:19:20+11:00
[INFO] Final Memory: 11M/38M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project gatk-tools: Could not resolve dependencies for project org.cruk.gatk:gatk-tools:jar:1.0-SNAPSHOT: Failed to collect dependencies at org.broadinstitute.gatk:gatk:jar:3.7: Failed to read artifact descriptor for org.broadinstitute.gatk:gatk:jar:3.7: Could not transfer artifact org.broadinstitute.gatk:gatk:pom:3.7 from/to bioinformatics (http://internal-bioinformatics.cruk.cam.ac.uk/maven): internal-bioinformatics.cruk.cam.ac.uk: nodename nor servname provided, or not known: Unknown host internal-bioinformatics.cruk.cam.ac.uk: nodename nor servname provided, or not known -> [Help 1]

And indeed, http://internal-bioinformatics.cruk.cam.ac.uk/maven/org/broadinstitute/gatk/gatk/3.7/gatk-3.7.pom is not reachable.

I'm not familiar with maven, so maybe I have something misconfigured. Can you please suggest how do I go on from here?

Hi,

I'm using Strelka2 to genotype normal:tumour and am interested in low frequency variants, using CalculateSNVMetrics as part of a pipeline to remove SNVs with fewer than 4X on the tumour ALT. As such, the measure VariantAlleleCount is pretty interesting, though I don't see how it's 4 in each instance. Could you give me more insight into how it's calculated please?

Thanks.

##look at 1:125142813_C/A
(Normal on left, tumour on right)
1 125142813 . C A . PASS DP=109;Depth=109;DepthControl=66;DistanceToAlignmentEnd=41.00;DistanceToAlignmentEndMAD=11.50;DistanceToAlignmentEndMedian=42.00;HomopolymerLength=2;LowMapQual=0.00;MMQSDiff=34.63;MMQSDiffMedian=41.00;MQ=60;MQ0=0;MapQualDiff=0.00;MapQualDiffMedian=0.00;NT=ref;QSS=36;QSS_NT=36;ReadCount=108;ReadCountControl=66;ReadPosRankSum=-0.05;ReferenceStrandBias=0.439;Repeat=4;SGT=CC->AC;SNVSB=0;SOMATIC;SomaticEVS=7.45;StrandBias=0.454;TQSS=1;TQSS_NT=1;VariantAlleleCount=4;VariantAlleleCountControl=1;VariantAlleleFrequency=0.037;VariantAlleleFrequencyControl=0.015;VariantBaseQual=32.75;VariantBaseQualMedian=39.00;VariantMMQS=45.75;VariantMMQSMedian=41.00;VariantMapQual=60.00;VariantMapQualMedian=60.00;VariantStrandBias=0.500 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 65:1:0:0:1,1:63,65:0,0:0,0 43:0:0:0:3,3:40,40:0,0:0,0

##looked at another site: 10:96037571_A/T
10 96037571 . A T . PASS DP=90;Depth=90;DepthControl=49;DistanceToAlignmentEnd=48.50;DistanceToAlignmentEndMAD=8.00;DistanceToAlignmentEndMedian=45.50;HomopolymerLength=4;LowMapQual=0.00;MMQSDiff=12.57;MMQSDiffMedian=4.00;MQ=60;MQ0=0;MapQualDiff=0.00;MapQualDiffMedian=0.00;NT=ref;QSS=38;QSS_NT=38;ReadCount=87;ReadCountControl=47;ReadPosRankSum=0.51;ReferenceStrandBias=0.362;Repeat=4;SGT=AA->AT;SNVSB=0;SOMATIC;SomaticEVS=8.96;StrandBias=0.379;TQSS=1;TQSS_NT=1;VariantAlleleCount=4;VariantAlleleCountControl=1;VariantAlleleFrequency=0.046;VariantAlleleFrequencyControl=0.021;VariantBaseQual=32.75;VariantBaseQualMedian=39.00;VariantMMQS=19.50;VariantMMQSMedian=4.00;VariantMapQual=60.00;VariantMapQualMedian=60.00;VariantStrandBias=0.250 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 49:1:0:0:48,48:0,0:0,0:0,1 40:2:0:0:35,37:0,1:0,0:3,3