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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