CombineGVCFs Fails for a batch of 2 samples where samples shows high number of alternate INDEL Alleles

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info 2020

• April 29, 2020 20:24

 

Hello GATK-Team,

A similar problem has been reported before, however couldn't solve for my case---

https://gatkforums.broadinstitute.org/gatk/discussion/4898/java-lang-arrayindexoutofboundsexception-in-genotypegvcfs-when-multi-threading

I ran the following command on a 2 sample set with GATK latest and GATK-3.6.0 to combineGVCF files for the contig hs37d5

../bin/gatk-4.1.7.0/gatk CombineGVCFs -R /scratch/HS_Build37/BWA_INDEX_hs37d5/hs37d5.fa -V IPF0047.194173.endPosCorr.gvcf.gz -V IPF0048.194174.endPosCorr.gvcf.gz-L hs37d5 -O cohort.2.3.newGATK.hs37d5.gvcf

and 

java -jar /nfs/goldstein/software/GATK/GATK-3.6.0-ArchivedVersion-g89b7209-patched/GenomeAnalysisTK.jar -T CombineGVCFs -R /scratch/HS_Build37/BWA_INDEX_hs37d5/hs37d5.fa -V IPF0047.194173.endPosCorr.gvcf.gz -V IPF0048.194174.endPosCorr.gvcf.gz -L hs37d5 > cohort.2.2.hs37d5.txt

The ERROR message received:

 

 

CombineGVCF was succesful till hs37d5:24140804 and Failed at hs37d5:24140805. I think the error is because of a site with higher number of Alternate Indel Alleles in 1 sample --

Screen shot of hs37d5:24140805 in Sample2

........

 

Would really appreciate any help in this regard...

Thanks!

 

 

 

 

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• 

  Bhanu Gandham

  • April 30, 2020 16:07

  Can you please post the error message using the latest version since we do not support GATK3 anymore. 

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  info 2020

  • April 30, 2020 16:48

  Error from gatk-4.1.7.0--

  

   

   

   

   

   

   

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• 

  Bhanu Gandham

  • May 12, 2020 21:01

  Hi info 2020

   

  Can you please share the two gvcfs with us so we can reproduce the error on our end. You can find instructions to sharing our data here: https://gatk.zendesk.com/hc/en-us/articles/360035889671

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