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-d debug [false]
-d debug [false]
-q do not print options and summary [false]
-q do not print options and summary [false]
-n do not fail when REF is inconsistent with reference sequence for non SNPs [false]
-m exits when REF is inconsistent with
unmasked reference sequence for non SNPs.
This overides the -n option [false]
-n warns but does not exit when REF is inconsistent
with reference sequence for non SNPs [false]
-w window size for local sorting of variants [10000]
-w window size for local sorting of variants [10000]
-I file containing list of intervals []
-I file containing list of intervals []
