Fix multisample VCF for unaligned positions

tseemann / ekidna

Assembly based core genome SNP alignments for bacteria

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Fix multisample VCF for unaligned positions #9

Open tseemann opened 5 years ago

tseemann commented 5 years ago

Currently the ekidna.vcf is made by merging all the variant VCF files. But these are ignorant of unaligned regions. Need to somehow put . in the positions for samples with no consensus?