GitHub - yandgong307/SNP_calling_pipeline: Pipeline for variant calling from single-cell RNA-seq data

SNP calling pipeline

Lincoln Harris
CZ Biohub, October 2018

Implements high-throughput variant calling on scRNA-seq data. Also contains analysis tools for various down-stream data-processing tasks.

Name		Name	Last commit message	Last commit date
Latest commit History 314 Commits
bulkAnalysis		bulkAnalysis
coverage		coverage
gatk		gatk
getMutationCounts		getMutationCounts
lolliplots		lolliplots
mutationCountsTable		mutationCountsTable
processVCFs		processVCFs
py_notebooks		py_notebooks
r_notebooks		r_notebooks
reflow		reflow
removeDups		removeDups
summaryTable		summaryTable
.gitignore		.gitignore
Dockerfile		Dockerfile
LICENSE		LICENSE
Makefile		Makefile
README.md		README.md
cDNA_plate_metadata.csv		cDNA_plate_metadata.csv
download_data.sh		download_data.sh
gatk.nf		gatk.nf
metadata_all_cells_4.10.19.csv		metadata_all_cells_4.10.19.csv
summaryMetadata_4.10.19.csv		summaryMetadata_4.10.19.csv