QuinnC ✭
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An update: I tried this with gatk 4.0.12.0 and it worked!
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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 referenc…
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Hi @bhanuGandham, The file is called twovcfs1.tar.gz. Thank you!
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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 yo…
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Hi @bhanuGandham Thanks for looking into this! Here are the first 10 lines for my interval.00.list: ctg7180024710462 ctg7180024952859 ctg7180025043953 ctg7180024953445 ctg7180024780449 ctg7180024953454 ctg7180024361837 ctg7180024716175 ctg71…
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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…
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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
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Thank you, Mauro! Will upgrade to 4.0.6.0 and give it a try!
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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…