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From: Kazmierczak S. <ste...@gm...> - 2017-03-24 22:21:01
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I just use the --missing-site on a cohort VCF and it seems your code is reporting single 0 (reference) and dot (.) in case of 1/. as missing ???? The 0 alone should not be report as missing right ? the reference mean the sample as a normal allele. Reporting it as missing doesn't make sense and If reference is missing then dot which is an error/miss call is different, they can not be count as the same thing |