
Genevieve Brandt (she/her)
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Activity overview
Latest activity by Genevieve Brandt (she/her)-
Genevieve Brandt (she/her) commented,
Hi Zane Swaydan, I think I've found a related issue, which came up in GATK 4.2.4.0: https://github.com/broadinstitute/gatk/issues/7639 and has since been solved. Could you try creating your Genomic...
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Genevieve Brandt (she/her) commented,
Hi Matthew Lueder, Yes, if your data has UMIs, the only step this will change is the MarkDuplicates step. You will need to perform UMI-aware read deduplication. I am not familiar with the other too...
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Genevieve Brandt (she/her) commented,
Hi Kevin Nathanael Ramanto, There's no option for this distinction. If a site is homozygous reference and force called, there was no variant at that site. Also, generally sites with a QUAL score lo...
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Genevieve Brandt (she/her) commented,
Barbara Iadarola Leonardo Vincenzi thank you for your patience while we looked into this question. CollectHsMetrics filters for base quality 20 and mapping quality 20 as default. These parameters a...
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Genevieve Brandt (she/her) commented,
Hi Philipp Hähnel, There isn't a specific tool that can get this interval list for you. Your best bet would be to use DepthofCoverage and do some post processing. Please let us know if you have an...
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Genevieve Brandt (she/her) commented,
Hi Jakub S, Regarding SnpEff and functional annotations, VQSR doesn't use any functional annotations to make the model. You can use any annotations that you prefer. If you want all of the standard ...
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Genevieve Brandt (she/her) commented,
Priyam Patel we now have an updated Panel of Normals workflow that is slightly different than your comment. Please note it uses GenomicsDBImport and CreateSomaticPanelOfNormals instead of MergeVcfs.
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Genevieve Brandt (she/her) commented,
Hi LP, I'm glad you are seeing improvement when using the --linked-de-bruijn-graph option! The -linked-de-bruijn-graph option is relatively new so our developers are still determining if they want ...
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Genevieve Brandt (she/her) commented,
Hi EvanKristiansen, We would recommend that you use the older version of BWA (bwa aln), not BWA MEM if you have very short reads. MEM stands for minimum exact match, because the reads have to have ...
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Genevieve Brandt (she/her) commented,
Thanks for the update Bastiaan! Glad it's working.