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The SVAltAligner walker traverses a set of BAM files to compute alignments to the alternate alleles of structural variations. This walker is one component of the SVAltAlign pipeline.
-I <bam-file> : The set of input BAM files containing records to realign.
-altReference <fasta-file> : The fasta file for the alternate allele
reference sequences. The fasta file must be indexed with 'samtools faidx' or
the equivalent. This file should be the output from
-alignMappedReads : If present, then align all reads in the input BAM files,
not just unmapped reads (default false).
-alignUnmappedMates <true/false> : If true (the default), then align
unmapped mates of mapped reads (i.e. reads that have a reference position but
have the unmapped flag set). If set to false, then only reads in the
"unmapped" portion of the BAM file will be aligned.
-md <directory> : The metadata directory containing metadata about the
input data set.
-O <bam-file>: The output from this walker is a BAM file containing new alignments for input reads that align to the alternate allele reference sequences. If no output file is specified, the output is in SAM format instead and is written to standard output.
Geraldine Van der Auwera, PhD