phd-pipeline

Some workflows I wrote for my phd research projects:

Bioinformatics pipelines

• Data pre-processing for variant discovery GATK4

• GATK4 germline short variant discovery (SNPs + Indels)

• GATK4 call somatic snvs indels

• Mitochondrial short variant discovery (SNVs + Indels)

• SV pipelines

• CNV pipelines

• Mutational signatures

• Telomere length estimation

• Eigenetic clock

Association studies

• Epigenome-wide association study

• Genome-wide association study

• Methylation quantitative trait loci analysis

• Causal mediation analysis

• Create summary stats table

Data visualizations

• Chord diagram

• Correlation heatmap

• Heatmap shows overlapping CpGs of epigenetic clocks

• Correlation plots

• Regression coefficient and CI plot

• Meta-analysis funnel plot

• Meta-analysis forest plot

• Sample flow chart

• t-test boxplot

• Bidirectional Manhattan plot and QQ plot

• SNP CpG association

• Global ancestry PCA

Other

• Year one screening exam