9/16/2022
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.
Max
Isn't Maximum the greatest?
January 1, 2020
svtools [^paper] are the comprehensive utilities to explore structural variations in genomes [^svtools] Pythin version svtools requires Python 2.7. Installation [^install] My perso
3/31/2023
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
3/31/2023
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
3/31/2023
What tools can we use to do numerical integration? Python scipy.integrate Purpose Solve a double integral numerically. Installation Usage Examples 1. Simple single integral To calc
3/28/2023
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
3/28/2023
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
3/22/2023
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
3/22/2023
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
3/21/2023