Tiffany Miller
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Activity overview
Latest activity by Tiffany Miller-
Tiffany Miller commented,
Genevieve Brandt (she/her) this is the masked reference blog post you were referring to right? https://www.illumina.com/science/genomics-research/articles/dragen-demystifying-reference-genomes.html
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Tiffany Miller commented,
Hi Bernt, No worries and thanks for your responses. The latest comment in the bug thread from nalinigans says: "4.1.8.0 has a new option - --genomicsdb-shared-posixfs-optimizations for GenomicsDBIm...
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Tiffany Miller commented,
Hi Tom, We weren't able to replicate your results (aligned fastq with bwa and ran MD) - everything looked as expected. Could you share your pre- Mark Duplicates bam by following these instructions?
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Tiffany Miller commented,
Can you show us the mates of these reads?
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Tiffany Miller commented,
Can you extract all the reads with these two querynames NB551226:81:H273NBGXB:3:22406:1443:19094 and NB551226:81:H273NBGXB:2:22111:10308:4079 share it with us?
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Tiffany Miller commented,
Hey Tom! Ok, I will need to ask a few teammates and will report back.
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Tiffany Miller commented,
Hi Tom Morrison, Just curious, does it get removed if you use "remove all duplicates" ? --remove-all-duplicates - If true do not write duplicates to the output file instead of writing them with ...
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Tiffany Miller commented,
Hi @wd, sorry for the delay. It appears another user was having this issue and it was due to the sample names getting altered. Does this apply to your situation?
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Tiffany Miller commented,
Hi jhb Sorry for the delay, but here are responses to your questions: 1) Is the listing of allele depths from before local realignment a universal feature of the GATK pipeline, or is it something t...
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Tiffany Miller commented,
Hi marta r I am not able to replicate your error using gatk 4.1.7.0 Here are the commands I used and the way I set up the RefSeq file. We need to update the RefSeq doc b/c it isn't clear as to what...