Man pages for flow-r/ngsflows
Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr
| 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 |
