Scripts for MT mutation calling.


01_mtscATAC_preprocess.sh: Code for the preprocess of mtscATAC-seq datasets (PBMC from old donors).
01_scMulti_preprocess.sh: Code for the preprocess of scMulti-omics datasets (PBMC from young donors).
01_SS2_preprocess.sh: Code for the preprocess of Smart-seq2 datasets (T cells from CRC, T cells from autoimmune diseases and HSPC colonies).
02_SplitBam_10x.py: Code for splitting the bam generated by cellranger into individual bam files.
03_mtDNA_mutation_calling_10x.sh: Code for calling mtDNA mutations in single cells from 10x scATAC data.
03_mtDNA_mutation_calling_SS2.sh: Code for calling mtDNA mutations in single cells from Smart-seq2 data.
04_mtSNV_filter_real_datasets.ipynb: Code for calling/recalling of mtDNA mutations for single cells in real experimental datasets.
pileup_inf_rj.pl: Code for generating depth information for different loci.
