Man pages for ctDNAtools
Analyze Circulating Tumor DNA Sequencing Data

analyze_fragmentation	Provides fragment ends analysis
bin_fragment_size	Gets histogram of fragment lengths from a bam file
compare_simulated_observed	Compares simulated and observed variant allele counts
create_background_panel	Creates a background panel from a list of bam files
create_background_panel_instance	Creates a background panel instance from a bam file (e.g....
create_black_list	Creates a black list of genomic loci based on a background...
extract_trinucleotide_context	Extracts the trinucleotide context for a set of mutations
filter_mutations	Filters a set of mutations
get_background_rate	Computes the background mismatch rate from a bam file
get_bam_chr	Helper function to extract chromosome names from a bam file
get_bam_SM	Helper function to extract SM from a bam file
get_fragment_size	Gets fragment lengths from a bam file
get_hist_bins	Helper function to bin a variable
get_mutation_read_names	Gets names of the reads showing reference and alternative...
get_mutations_fragment_size	Gets reads fragment lengths for a list of mutations
get_mutations_read_counts	Counts ref and alt reads for a set of mutations
get_mutations_read_names	Gets names of the reads showing reference and alternative...
get_read_counts	Gets read counts for a specific locus in the genome
merge_mutations_in_phase	Collapses mutations in phase into one event
mutations	Example mutations data to use with ctDNAtools package
positivity_test	Computes a p-value of ctDNA positivity with a Monte-Carlo...
simulator	A function to sample from binomial distribution
summarize_fragment_size	Summarizes fragment size in defined genomic regions
targets	Example Genomic targets to use with ctDNAtools package
test_ctDNA	Tests the ctDNA positivity of a sample
vcf_to_mutations_df	Helper function to read a vcf into the required format of...
verify_tag	Helper function to verify a tag exists