annotate | Generates a cmdline, when invoked annotates files using... |
annotate_mutect | annotate_mutect |
annotate_variants | annotate variants |
annotate_vcf | Not tested |
avail_genomes | Use Illumina's iGenomes and get a list of available genomes |
bwa | Wrapper for BWA sequence alignment tool |
check_fastq_sheet | check_fastq_sheet |
chipseq | A complete chipseq pipeline from fastq to MACS and Scripture |
chk_fq | chk fq: |
create_fq_sheet | create a sheet of fastq |
create_sample_sheet | Creates a sample sheet file names in the provided folder |
fastqc | Fastqc |
fetch_genomes | fetch_genomes |
get_fasta_chrs | Read the associated dictionary file and return a list of... |
get_fq_ext | get extention of fastq files |
haplotyper | a wrapper around gatk haplotyper |
merge_sheets | Title |
modules | Show a list of all available modules in NGSFlows |
mutect | A wrapper around somatic mutation caller MuTect |
parse_somatic_vcf | Parse a somatic VCF, with two samples. |
parse_vcf | Parse a VCF file into a TSV to be processed and annotated |
picard_bam_fastq | Title |
picard_merge | Use picard's MergeSamFiles tool to merge bam/sam files |
picard_reorder | Use picard's MergeSamFiles tool to merge bam/sam files |
picard_rg | picard_rg |
preprocess | Pre-process bam files following Broad's best practices for... |
samtools | set of wrapper functions around samtools |
split_fq | split fastq into pre-determined number of splits |
split_names_fastq | split.names.fastq |
split_names_fastq2 | split_names_fastq2 |
star | A flowr wrapper for STAR aligner |
star_index | star_index |
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