
Shaun Clare
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Activity overview
Latest activity by Shaun Clare-
Shaun Clare commented,
Hey, It took me a while to upgrade to WSL2 but it looks like it finished GenotypeGVCF this time. Thank you!!
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Shaun Clare created a post,
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...
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Shaun Clare commented,
I did find this with someone saying they found a work around using unzipped g.vcf but I'm not sure if that's just to get into GenomicsDB? I was working with unzipped g.vcf anyway and it didn't work...
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Shaun Clare created a post,
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...
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Shaun Clare commented,
I managed to fix it by modifying ls to write as one column using: ls -1 *.sorted.bam | <rest of command> I'm not sure why it worked in the first place, or maybe I accidentally deleted part of my co...
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Shaun Clare created a post,
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...
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Shaun Clare commented,
Unfortunately since its 44k separate amplicons, --merge-input-intervals wasn't able to work since it can't detect if they were abutting. I used --merge-contigs-into-num-partitions 50 instead and I ...
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Shaun Clare commented,
It seems to be working but I'm guessing this is going to take a long time. It got passed initializing the engine but gave a warning to not use more than 100 intervals, this uses 44,000 amplicons as...
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Shaun Clare commented,
Our pipeline was built using CombineGVCFs along time ago so I was familiar with it. Isn't the intervals option required to make the GenomicsDB datastore? I just want all SNP across the whole 'genome'
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Shaun Clare created a post,
Issue with combining g.vcf files
AnsweredI 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 ...