Generate an alternative reference sequence over the specified interval
java -jar GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R reference.fasta -o output.fasta -L input.intervals -V input.vcf [--snpmask mask.vcf]
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--variant  -V | NA | Input VCF file | |
Optional Inputs | |||
--snpmask | none | SNP mask VCF file | |
Optional Outputs | |||
--out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
Optional Parameters | |||
--lineWidth  -lw | 60 | Maximum length of sequence to write per line | |
--use_IUPAC_sample  -IUPAC | NA | If specified, heterozygous SNP sites will be output using IUPAC ambiguity codes given the genotypes for this sample | |
Optional Flags | |||
--rawOnelineSeq  -raw | false | Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity) | |
--snpmaskPriority | false | SNP mask priority |