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

Illumina / PlatinumGenomes

The Platinum Genomes Truthset

https://illumina.github.io/PlatinumGenomes

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Open blmoore opened 6 years ago

blmoore commented 6 years ago

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