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edolzhenko committed Jan 17, 2019
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Expansion Hunter requires an indexed BAM or a CRAM file containing aligned reads
from a PCR-free WGS sample, a FASTA file with a reference genome assembly (which
must be the same as the one used to align the reads), and a [variant catalog
file](04_VariantCatalogs.md).
file](04_VariantCatalogFiles.md).

Expansion Hunter outputs a VCF file and a JSON file with repeat genotypes along
with other useful information and a log file with alignments of spanning and
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to search for informative reads. Set to 1000 by default.

Note that the full list of program options with brief explanations can be
obtained by running `ExpansionHunter --help`.
obtained by running `ExpansionHunter --help`.

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