Category

Genome Variant Analysis


Usage

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


Manual

Argument name(s)Default valueSummary
Required Inputs
--variant
 -V
NAInput VCF file
Optional Inputs
--snpmask
noneSNP mask VCF file
Optional Outputs
--out
 -o
stdoutAn output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--lineWidth
 -lw
60Maximum length of sequence to write per line
--use_IUPAC_sample
 -IUPAC
NAIf specified, heterozygous SNP sites will be output using IUPAC ambiguity codes given the genotypes for this sample
Optional Flags
--rawOnelineSeq
 -raw
falsePrint sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity)
--snpmaskPriority
falseSNP mask priority


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