Hugo DENIS
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Activity overview
Latest activity by Hugo DENIS-
Hugo DENIS commented,
Hi, Thank you for your answer. It therefore seems that this tool would not suit our target species. If genotype qualities are well calibrated, I also noticed something odd in our vcf file produce...
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Hugo DENIS commented,
Hi, Thank you again for your help. I created the vcf file using GATK best practice pipeline : 1 HaplotypeCaller > (all reference) 2 GenomicDBimport > Create genomic database (chromosomes only, sp...
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Hugo DENIS created a post,
Can CalculateGenotypePosteriors be used on hard-filtered VCF
Hi, I was wondering if it is possible/makes sense to use CalculateGenotypePosteriors tool on a hard-filtered multi-sample vcf file ? I have a large multi-sample vcf file (>800 individuals) from a...
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Hugo DENIS created a post,
Is it recommended to filter out SNPs around INDELS ?
Hi, thanks a lot for this amazing tool, I have seen in different variant filtration pipelines people recommending to remove/mask SNPs that are located close to INDELs (e.g., 5-10 bp from INDELS po...
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Hugo DENIS commented,
Dear Gökalp, Thank you very much for your help. When specifying -L ${CONTIG} it works perfectly, as long as the working directory is not the same as the one where the GenomicsDBImport folder is ...
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Hugo DENIS created a post,
GenotypeGVCFs issue when using --include-non-variant-sites parameter
Hi, I am running similar issues as in this post : https://github.com/broadinstitute/gatk/issues/8415 but I am reposting here as it seems this is a more convenient place to get an answer. I am run...
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Hugo DENIS commented,
Dear Gökalp, I managed to install docker and gatk docker image and it works perfectly now. Thank you for your help, Best
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Hugo DENIS commented,
Hi, Thank you for your responsiveness. Docker is not installed on the cluster I am working with, I have asked administrators about it. In the meantime I tried to use the last github master branch...
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Hugo DENIS commented,
Hi again, I have tried running the same code and inputs on a different machine and it worked which tends to suggest that the issue is indeed related to dependencies conflicts. I have seen this po...
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Hugo DENIS commented,
Hi, thank you for your answer. I tried your suggestions, changing the destination drive and adding the option, as well as increasing the number of samples, but unfortunately it does not seem to so...