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Shaun Clare

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  • Error in GenotypeGVCF: Cannot read tile from file

    REQUIRED for all errors and issues: a) GATK version used: 4.3.0.0 b) Exact command used:  set=CBref=V_macrocarpon_Stevens_v1gatk --java-options "-Xmx12g" GenotypeGVCFs \   -R ${ref}.fasta \   -V ge...

  • Issue with GenomicsDBImport on very large chromosomes

    So I'm having the following issue. I managed to import all of samples into GenomicsDB and it all seemed to work fine. However, when running GenotypeGVCFs on certain chromosomes the engine shuts dow...

  • Cannot parallelize GATK

    So I am rather confused what is going on, I am trying to use HaplotyperCaller to genotype ~1100 samples. I ran this is exact code on the entire set, getting through ~800 when it was actively workin...

  • Issue with combining g.vcf files

    Answered

    I have an issue with combining my g.vcfs. It is 96 samples called against an amplicon based reference so it's approximately 38k (called the 50k) sequences of 250 bp or less. These codes previously ...

  • CombineGVCFs

    Answered

    So I noticed I was having trouble combining my g.vcf files, which is saying my index is out of bounds. My HaplotypeCaller command seemed to work fine and all of these codes work fine when I use amp...

  • Invalid or corrupt jar file

    Answered

    I'm getting an invalid or corrupt .jar file error. I found somehow my java had switched to 11 but I changed that back to 8. Also, I switched to a miniconda install where 'gatk -help' actually provi...