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hg19 release VCF contig order does not match VCF header / hg19 fasta #1

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blmoore opened this issue Oct 26, 2017 · 0 comments
Open

hg19 release VCF contig order does not match VCF header / hg19 fasta #1

blmoore opened this issue Oct 26, 2017 · 0 comments
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@blmoore
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blmoore commented Oct 26, 2017

Some tools care about this, expected ordering is natural sort (1-22 + X).

Workaround is to sort with bcftools:

bcftools sort NA12878.vcf.gz -Oz -o NA12878.sorted.vcf.gz
@blmoore blmoore added the bug label Oct 27, 2017
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