Sheryl
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Activity overview
Latest activity by Sheryl-
Sheryl commented,
Thanks for your reply David Benjamin. Oh right - I'm not sure this is the message that comes across from the documentation, e.g. Mutect2.scatter_count -- Number of executions to split the Mutect2...
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Sheryl created a post,
somatic CNV PoN
Hi, I'm using GATK 4.3.0. I was wanting to create my own PON for CNV analysis. I have no matched normals and I'm using a different sequencing technology to Illumina. I was wondering if it was poss...
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Sheryl created a post,
Mutect2 wdl interval list and scatter count
REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: Hi, I am using GATK v4.3.0 and the mutect2.wdl for whole genome analysis. I have found a wgs...
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Sheryl commented,
I'm getting a similar sounding issue with Mutect2, the interval list file was passed to the inputs.json for the mutect2.wdl "Mutect2.split_intervals_extra_args": "-XL wgs_calling_regions.hg38.int...
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Sheryl commented,
Another consideration of course is that these databases are biased against any population that have little database representation e.g. indigenous populations
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Sheryl commented,
Conrad Leonard did you get any response to this? I think it's an interesting point and one which I would like to get advice on from the GATK team
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Sheryl created a post,
Best practice trios
I am a newbie at WES and Trios. I have run some uBAMs from Mum, Dad, Child through ExomeGermlineSingleSample_v3.1.7. I now want to end up with a 'best pratice' vcf for the trio. I came across this ...
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Sheryl commented,
Apologies...it is here: https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0;tab=objects?prefix=&forceOnObjectsSortingFiltering=false Not here: https://console.c...
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Sheryl created a post,
Where can I download Homo_sapiens_assembly38.haplotype_database.txt
Hi, I am trying to run WholeGenomeSingleSample_v3.1.8 for the first time and cannot locate the Homo_sapiens_assembly38.haplotype_database.txt It is NOT in "gs://gcp-public-data--broad-references...