gatk FastaAlternateReferenceMaker

Reference

Generate an alternative reference sequence over the specified interval

Category

Genome Variant Analysis

Usage

gatk FastaAlternateReferenceMaker [options] -R reference.fasta -O output.fasta -L input.intervals -V input.vcf

java -jar GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R reference.fasta -o output.fasta -L input.intervals -V input.vcf [--snpmask mask.vcf]

Manual

Required Arguments

  • --output string: Path to write the output fasta to.
  • --reference string: Reference sequence file (FASTA format). GATK also expects a genome dictionary for the sequence file, see CreateSequenceDictionary for instructions.
  • --variant string: A source of variants to merge with the reference sequence (VCF format).

Options

  • --arguments_file: Read one or more arguments files and add them to the command line.
  • --cloud-index-prefetch-buffer int: Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
  • --cloud-prefetch-buffer int: Size of the cloud-only prefetch buffer (in MB; 0 to disable).
  • --disable-bam-index-caching: If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
  • --disable-sequence-dictionary-validation: If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
  • --gcs-max-retries int: If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection.
  • --gcs-project-for-requester-pays: Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
  • --help: Display the help message.
  • --interval-merging-rule samp: Interval merging rule for abutting intervals.
  • --intervals samp: One or more genomic intervals over which to operate.
  • --line-width int: Maximum length of sequence to write per line.
  • --sites-only-vcf-output: If true, don't emit genotype fields when writing vcf file output.
  • --snp-mask string: SNP mask VCF file.
  • --snp-mask-priority: Give the snp mask priority over the input VCF.
  • --use-iupac-sample: If specified, heterozygous SNP sites will be output using IUPAC ambiguity codes given the genotypes for this sample.
  • --version: Display the version number for this tool.
  • --add-output-sam-program-record: If true, adds a PG tag to created SAM/BAM/CRAM files.
  • --add-output-vcf-command-line: If true, adds a command line header line to created VCF files.
  • --create-output-bam-index bool: If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
  • --create-output-bam-md5 bool: If true, create a MD5 digest for any BAM/SAM/CRAM file created.
  • --create-output-variant-index bool: If true, create a VCF index when writing a coordinate-sorted VCF file.
  • --create-output-variant-md5 bool: If true, create a a MD5 digest any VCF file created.
  • --disable-read-filter samp: Read filters to be disabled before analysis.
  • --disable-tool-default-read-filters: Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on).
  • --exclude-intervals samp: One or more genomic intervals to exclude from processing.
  • --gatk-config-file string: A configuration file to use with the GATK.
  • --input samp: BAM/SAM/CRAM file containing reads.
  • --interval-exclusion-padding int: Amount of padding (in bp) to add to each interval you are excluding.
  • --interval-padding int: Amount of padding (in bp) to add to each interval you are including.
  • --interval-set-rule samp: Set merging approach to use for combining interval inputs.
  • --lenient: Lenient processing of VCF files.
  • --QUIET: Whether to suppress job-summary info on System.err.
  • --read-filter samp: Read filters to be applied before analysis.
  • --read-index samp: Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
  • --read-validation-stringency samp: Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
  • --seconds-between-progress-updates float: Output traversal statistics every time this many seconds elapse.
  • --sequence-dictionary string: Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
  • --tmp-dir string: Temp directory to use.
  • --use-jdk-deflater: Whether to use the JdkDeflater (as opposed to IntelDeflater).
  • --use-jdk-inflater: Whether to use the JdkInflater (as opposed to IntelInflater).
  • --verbosity samp: Control verbosity of logging. Supported levels: ERROR, WARNING, INFO, DEBUG
  • --showHidden: Display hidden arguments.

File formats this tool works with
VCF

Share your experience or ask a question