The GenerateAltAlleleFasta utility processes a VCF file to extract the sequences of the alternate alleles.
For each structural variation record in the VCF, this utility will generate
one output sequence in fasta format for each alternative allele that has
precise breakpoints. The identifier for the alternate allele will be
alleleNumber is the number of the allele
in the ALT column of the VCF file (the first ALT allele is allele 1).
The remainder of each fasta header line after the ID contains an encoded description of how the allele sequence maps back to the reference genome. The naming convention for the fasta sequences and the format of the rest of the header line is understood by other programs that use the alternate allele fasta file as input.
Here is an example of a generated fasta header:
This example us for the first alternate allele of a variant with
ID P2_M_061510_20_81. The length of the generated fasta sequence is 401 bases.
Bases 1-200 of the alternate allele sequence aligns to chr20:51913435-51913634
of the reference sequence and bases 202-401 of the fasta sequence aligns to
bases chr20:51913736-51913935 of the reference sequence. Thus, this event
represents a deletion of 101bp of the reference (chr20:51913635-51913735) with
one base of non-template sequence present in the alternate allele.
-I <vcf-file> : The input VCF file.
-R <fasta-file> : Reference sequence. An indexed fasta file containing
the reference sequence. The fasta file must be indexed with 'samtools faidx'
or the equivalent.
-flankLength <N> : The number of reference bases to include around each
alternate allele (default 200). The flank length is counted outside of any
micro-homology around the breakpoints.
-O <fasta-file>: An output fasta file containing one entry for each alternative structural allele. The default is to write to stdout.