
Shaun Clare
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Recent activity by Shaun Clare Sort by recent activity-
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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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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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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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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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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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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I do have another issue on another project. This one uses the exact same codes but it's on 96 samples called against a much smaller amplicon based reference. gatk CombineGVCFs --java-options "-Xmx...
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Genevieve Brandt (she/her) Thank you, that seems to have worked!
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Running GATK worked fine and that code had worked previously. I couldn't find the error so I rebuilt my Ubuntu from scratch a while ago and it fixed everything so the code works again. Thanks, Shaun