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I have been rerunning my torture test since issues I posted earlier have apparently been addressed.
The test:
1. generates random genomes and simulates reads from those genomes parameterizable in ma…
biork updated
2 years ago
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As they are returned, evaluate other general quality metrics from GP and DSP, for things like contamination and coverage and any/other picard metrics. Will update this ticket as I learn more about wha…
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I am mapping some FASTQs using a built-from-source dragen-os on:
wget "ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/p13/hg38.p13.fa.gz" with MD5
9930e3071308dc5e9b546934b43a2323 hg38.p13…
biork updated
2 years ago
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- Whatshap - 1.7, Python - 3.10.8
- Conda
- Which command-line parameters you used
- whatshap haplotag -o haplotaggedchr22.bam --reference Homo_sapiens_assembly38.fasta --region chr22 phased.vcf.…
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`chr9 22631432 Minda_146 N . PASS SVLEN=308438;SVTYPE=DUP;SUPP_VEC=ILL_MantaDUP:TANDEM:154784:0:1:0:0:0,ILL_gridss156bf_714h,PB_severus_DUP7420,ONT_severus_DUP8542,PB_ID_34921_2,ILL_2280402139:2,PB_r…
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One major curiosity about the new DRAGEN callset is the fact that it imputes the biological sex of samples and makes their sex chromosome calls haploid as appropriate, or marks them with a 'PloidyConf…
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`chr18 28481424 Minda_60 N ]chrX:95812868]N . PASS SVLEN=-1;SVTYPE=BND;SUPP_VEC=PB_severus_BND2976_2,PB_ID_40283_2,ONT_severus_BND3369_2,ONT_ID_69368_2,PB_r_192_1,ONT_r_114_1,ILL_gridss260fb_8331h,ILL…
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Good morning,
Our team is currently working to add Pelops to our bioinformatics pipeline. Specifically, we would like to use it within an internally developed tool that currently accepts VCFs and a…
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**Is your feature request related to a problem? Please describe.**
We need to understand, which code paths influence mehari performance.
**Describe the solution you'd like**
Use `flamegraph`, `DH…
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I know I can specify the [instance types](https://aws.github.io/amazon-genomics-cli/docs/concepts/contexts/#instance-types) for a specific context, which are available to all tasks, but I would also l…