ngsutilsj

ngsutilsj - Data wrangling for NGS
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Usage: ngsutilsj cmd [options]

Available commands:
[bam]
  bam-basecall     - For a BAM file, output the basecalls (ACGTN) at each genomic position.
  bam-best         - With reads mapped to two bam references, determine which reads mapped best to each
  bam-bins         - Quickly count the number of reads that fall into bins (bins assigned based on 5' end of the first read)
  bam-check        - Checks a BAM file to make sure it is valid
  bam-concat       - Concatenates BAM files (handles @RG, @PG)
  bam-count        - Counts the number of reads for genes (GTF), within a BED region, or by bins (--gtf, --bed, or --bins required)
  bam-coverage*    - Scans an aligned BAM file and calculates the number of reads covering each base
  bam-discord      - Extract all discordant reads from a BAM file
  bam-dups         - Flags or removes duplicate reads
  bam-expressed    - For a BAM file, output all regions with significant coverage in BED format.
  bam-filter       - Filters out reads based upon various criteria
  bam-readgroup    - Add a read group ID to each read in a BAM file
  bam-sample*      - Create a whitelist of read names sampled randomly from a file
  bam-split        - Split a BAM file into smaller files
  bam-stats        - Stats about a BAM file and the library orientation
  bam-tobed*       - Writes read positions to a BED6 file
  bam-tobedgraph   - Calculate coverave for an aligned BAM file in BedGraph format.
  bam-tofastq      - Export the read sequences from a BAM file in FASTQ format

[bed]
  bed-clean        - Cleans score entries to be an integer
  bed-count        - Given reference and query BED files, count the number of query regions that are contained within each reference region
  bed-nearest      - Given reference and query BED files, for each query region, find the nearest reference region
  bed-reduce       - Merge overlaping BED regions
  bed-resize       - Resize BED regions (extend or shrink)
  bed-tobed3       - Convert a BED3+ file to a strict BED3 file
  bed-tobed6       - Convert a BED6+ file to a strict BED6 file
  bed-tofasta      - Extract FASTA sequences based on BED coordinates

[fasta]
  fasta-filter     - Filter out sequences from a FASTA file
  fasta-gc         - Determine the GC% for a given region or bins
  fasta-genreads*  - Generate mock reads from a reference FASTA file
  fasta-mask       - Mask regions of a FASTA reference
  fasta-names      - Display sequence names from a FASTA file
  fasta-split      - Split a FASTA file into a new file for each sequence present
  fasta-subseq     - Extract subsequences from a FASTA file (optionally, indexed)
  fasta-tag        - Add prefix/suffix to FASTA sequence names
  fasta-wrap       - Change the sequence wrapping length of a FASTA file

[fastq]
  fastq-barcode    - Given Illumina 1.8+ naming, find the lane/barcodes included
  fastq-check      - Verify a FASTQ single, paired, or interleaved file(s)
  fastq-demux      - Splits a FASTQ file based on lane/barcode values
  fastq-filter     - Filters reads from a FASTQ file.
  fastq-merge      - Merges two FASTQ files (R1/R2) into one interleaved file.
  fastq-separate   - Splits an interleaved FASTQ file by read number.
  fastq-sort       - Sorts a FASTQ file
  fastq-split      - Splits an FASTQ file into smaller files
  fastq-stats      - Statistics about a FASTQ file
  fastq-tobam      - Converts a FASTQ file (or two paired files) into an unmapped BAM file
  fastq-tofasta    - Convert FASTQ sequences to FASTA format

[gtf]
  gtf-export       - Export gene annotations from a GTF file as BED regions
  gtf-geneinfo*    - Calculate information about genes (based on GTF model)

[annotation]
  annotate-gtf     - Annotate GTF gene regions (for tab-delimited text, BED, or BAM input)
  annotate-repeat* - Calculates Repeat masker annotations

[vcf]
  vcf-annotate     - Annotate a VCF file
  vcf-chrfix       - Changes the reference (chrom) format (Ensembl/UCSC)
  vcf-export       - Export information from a VCF file
  vcf-filter       - Filter a VCF file
  vcf-tobed        - Export allele positions from a VCF file to BED format

[help]
  help             - Help for a specific command
  license          - Show the license

* = experimental command