Workflow for generating IGV screenshots in Terra

Mosaic detection pipeline workflow

Annotate and filter de novo variants

Detect mosaic variants from filtered de novo variant callset (sample set)

Call de novo variants on a per-sample basis from proband, father, mother gvcfs

Apply a set of filters to the annotated de novo callset generated by annotate_variants

Annotate raw de novo variants generated by gvcf_to_denovo using VEP

Test read_tsv() functionality for processing large cohorts from sample tsv containing columns for ids, google bucket paths, etc

Test functionality of Object type

Call de novo SNVs for an individual given sample map and pedigree

Enable access to google bucket files within WDL task via gcsfuse mount

Takes as input an array of single-sample gvcf files, merges them using bcftools, then estimates cohort allele frequency on the basis of genotype information

Merge gVCF files using bcftools

workflow file for running BamToUnmappedBam conversion on multiple BAM files

workflow file for running CramToBam conversion on multiple CRAM files

A tool to identify ethnicity given a vcf file and to generate ethnic population-specific reference genomes

My code for BENG182: Biological Databases

Code from my CSE151: Machine Learning class assignments

My code from BENG181: Molecular Sequence Analysis assignments