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before a call is made. Without the --strict option, reads for individuals below the threshold are ignored.
before a call is made. Without the --strict option, reads for individuals below the threshold are ignored.
--minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.
--minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.
--maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.
--maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.
=== VCF Output ===
--glfAliases ''filename'' By default, GLF filenames are used to label each column in the VCF file. This option allows each filename
to be matched to a more specific individual identifier. The aliases file should include two columns per row,
the first specifying the VCF filename, the second specifying a sample name.
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