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Genotypegvcfs 3 Week Estimated Run Time for WGS

Hello all,

I am currently running Genotypegvcfs on 86 human WGS using GATK 3.7 and I am experiencing an estimated run time of 3+ weeks. My code is:

java -Xmx120G -Djava.io.tmpdir=/mnt/data_schen/travis/WGS-86/tmp -jar /mnt/data2/travis/bin/gatk_3.7\GenomeAnalysisTK.jar \
-T GenotypeGVCFs \
-R /mnt/data2/travis/REFERENCE/human_g1k_v37_decoy.fasta \
--variant WGS_86.list \
--disable_auto_index_creation_and_locking_when_reading_rods \
-newQual \
-o WGS_86.vcf

I am using GATK 3.7 to keep my pipeline consistent as I plan on combining these 86 with another 101 WGS samples that were run last year. HTC was used to generate gvcfs for each of the 86 individuals.

When run in multi-thread mode the application crashed with the "Code exception" error. This is very unfortunate as it had an estimated run time of 6 days.

I have read that you suggest running Genotypegvcfs in parallel by separating gvcfs based on chromosome. Do I need to:

  1. Separate every gvcf of every sample into 22 chromosomes + sex chromosomes (i.e. 187x24) with SelectVariants
  2. Combine the chromosomes using Combinegvcfs
  3. Run each chromosome separately through Genotypegvcfs
  4. Then combine the chromosomes using CatVariants

I am uncertain I fully understand the current recommendations and am looking for advice before moving forward. Are there any alternative methods I may consider?

Thank you

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie admin


    You can use -L to restrict your run to a single chromosome.

    You can also try combining the GVCFs with CombineGVCFs before GenotypeGVCFs. (Perhaps try 10 GVCFs at a time).


  • mizetravmizetrav Member

    GATK 3.8-1 was able to handle multi-thread mode greatly decreasing overall run time. Thank you very much!

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