suzy_bunters
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Activity overview
Latest activity by suzy_bunters-
suzy_bunters commented,
Hi Genevieve, it's now running in the format you suggested, thank you. Each job I submit to the cluster sits in a queue for hours, so testing different formats was taking a long time!
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suzy_bunters created a post,
A USER ERROR has occurred: Badly formed genome unclippedLoc
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.0.10.1 b) Exact command used: gatk --java-options "-Xmx4G -XX:+UseParallelGC -XX:ParallelGCThreads=2" HaplotypeCalle...
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suzy_bunters commented,
Hi Genevieve Brandt (she/her), There are no @RG lines in the header (the headers either start with @HD, @SQ, or @PG). The original fasta files from which the bam was generated were trimmed using Tr...
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suzy_bunters commented,
Hi Genevieve, thanks for your reply (and sorry to nag) :D I checked the forum before posting but the other solutions I found don't work for me. I'll be more patient though!
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suzy_bunters commented,
Hi there, is anyone able to help on this?
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suzy_bunters created a post,
emit-ref-confidence error using single sample BAM
Answereda) GATK version used: 4.1.7.0 b) Exact command used: gatk HaplotypeCaller -R final.fasta -I ${sampleName}_markdup.bam -O /${sampleName}.g.vcf.gz -ERC GVCF c) Entire error log: A USER ERROR has occu...
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suzy_bunters commented,
No, this is the first time I've tried using GATK. It's very possible there was an issue two years ago that I didn't address - I'd only just started working with WGS and wasn't accustomed to working...
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suzy_bunters commented,
Hi Genevieve Brandt (she/her), Thanks so much for your reply. I have a couple of follow up questions, if you have the time! 1) Do you know of any reason why this could have happened, other than th...
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suzy_bunters created a post,
HaplotypeCaller - incompatible contigs (one scaffold only)
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.7.0b) Exact command used: gatk HaplotypeCaller -R final.fasta -I ${sampleName}_markdup.bam -O /${sampleName}.g.vcf....