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- about a loss of 11% of variant thought distinct.
- about a loss of 11% of variant thought distinct.
To normalize and remove duplicate variants:
vt normalize mills.genotypes.bcf -r ~/ref/vt/grch37/hs37d5.fa | vt mergedups - -o mills.normalized.genotypes.bcf
and you will observe that 3994 variants had to be left aligned and 1092 variants were removed.
The following will be slight faster: + denotes using of uncompressed bcf stream.
vt normalize mills.genotypes.bcf -r ~/ref/vt/grch37/hs37d5.fa -o + | vt mergedups + -o mills.normalized.genotypes.bcf
==Coding regions==
==Coding regions==
