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--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.
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=== X Chromosome Variant Calling ===
=== X Chromosome Variant Calling ===
--xStart ''sexChromosomeStart'' Start of the non-pseudo-autosomal portion of the X (2,709,521 bp in build 36)
--xStart ''sexChromosomeStart'' Start of the non-pseudo-autosomal portion of the X (2,709,521 bp in build 36)
--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)
--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)
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== Download ==
== Download ==
