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--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)
For NCBI genome build 36, you should use the settings --xChr X --xStart 2709521 --xStop 154584237
For NCBI genome build 37, you should use the settings --xChr X --xStart 2699520 --xStop 154931044
== Model for Variant Calling ==
== Model for Variant Calling ==
