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Yuwei Bao 鲍雨薇

Welcome to my personal website!

Student Journalist
I have 30 articles published on McMurry University's War Hawks Herald school newspaper.
Outstanding Graduate
Fun fact - I was on Abilene newspaper when I graduate from McMurry University in Aug,2020.
Isn't Maximum the greatest?
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Ms.HopeJanuary 1, 2020
About 1 min
Run Lumpy to get structural variants
LUMPY is a probabilistic framework for structural variant discovery. Installation Here, we are using LUMPY (v0.2.12). Test Usage Part I Pre-processing 1. Align the data using BWA-M

Yuwei Bao3/31/2023
About 2 min
Run Delly to get structural variants
Installation Using docker image which pulls the latest version (v1.1.6) by default.[^docker] Usage Input file Delly needs a sorted, indexed and duplicate marked bam file for every

Yuwei Bao3/31/2023
Less than 1 minute
Strelka (v2.9.10) [^Strelka] Purpose Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tum

Yuwei Bao3/28/2023
Less than 1 minute
Somatic Sniper
Here, we are learning how to use SomaticSniper to identify single nucleotide positions that are different between tumor and normal and further to filter variants using some provide

Yuwei Bao3/22/2023
Less than 1 minute
Here, we are learning how to use freebayes [^freebayes] to call SNVs and further to filter variants using vcflib [^vcflib] and vt [^vt] following Nick Riddiford 21 supplementary me

Yuwei Bao3/22/2023
About 2 min
GEM - mappability
GEM mappability [^GEM] is a tool to estimate genome mappability and here is a tutorial by Dmytro Kryvokhyzha [^GEM_tutorial]. Thanks to Nick Riddiford for sharing his insights and

Yuwei Bao3/21/2023
About 2 min