QuinnC ✭

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• An update: I tried this with gatk 4.0.12.0 and it worked! :)

  in GenomicsDBImport terminates after Overlapping contigs found error Comment by QuinnC March 15
• I got this error, when working with a manually generated fasta file. "ERROR MESSAGE: Bad input:We encountered a non-standard non-IUPAC base in the provided reference: '45'. It took a bit of panicked searching, but then I realised that the refer…

  in ERROR MESSAGE: Bad input:We encountered a non-standard non-IUPAC base in the provided reference: '13 Comment by QuinnC November 2018
• Hi @bhanuGandham, The file is called twovcfs1.tar.gz. Thank you! :)

  in GenomicsDBImport terminates after Overlapping contigs found error Comment by QuinnC November 2018
• Hi @bhanuGandham, Adding --genomicsdb-segment-size 100000000 still gives the protocol buffer error. These g.vcf files were generated using gatk4's HaplotypeCaller. I'd be happy to share my g.vcf files, how should I go about sharing them? Will you …

  in GenomicsDBImport terminates after Overlapping contigs found error Comment by QuinnC November 2018
• Hi @bhanuGandham Thanks for looking into this! :) Here are the first 10 lines for my interval.00.list: ctg7180024710462ctg7180024952859ctg7180025043953ctg7180024953445ctg7180024780449ctg7180024953454ctg7180024361837ctg7180024716175ctg7180025056092…

  in GenomicsDBImport terminates after Overlapping contigs found error Comment by QuinnC October 2018
• I have tried with the following: gatk GenomicsDBImport \--java-options "-Xmx250G -XX:+UseParallelGC -XX:ParallelGCThreads=24" \-V input.list \--genomicsdb-workspace-path 5sp_45ind_assmb_00 \--intervals interval.00.list \--batch-size 9 w…

  in Trouble getting combined gvcf file using either GenomicsDBImport or CombineGVCFs Comment by QuinnC October 2018
• Hi Sheila, Thank you for the inspiration! I'll try with --batchSize and splitting up the intervals (which is a list of contigs) instead of trying to combine everything at one go. Will update with my progress :) Cheers, Quinn

  in Trouble getting combined gvcf file using either GenomicsDBImport or CombineGVCFs Comment by QuinnC August 2018
• Thank you, Mauro! Will upgrade to 4.0.6.0 and give it a try!

  in (How to) Consolidate GVCFs for joint calling with GenotypeGVCFs Comment by QuinnC August 2018
• I am currently using GATK 4.0.5.1 and looking to analyse SNPs from a target capture dataset done on a non-model organism without linkage or chromosome information. There are 2900 targeted regions/contigs each across 45 individuals. I have run Haplot…

  in (How to) Consolidate GVCFs for joint calling with GenotypeGVCFs Comment by QuinnC August 2018