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Outdated version of bcftools in dockerfile: "Unsorted positions", position 0 vs. 4294967296
Version 1.11 of bcftools in the brentp/smoove:bdf809472b6a
docker image doesn't support 0 coordinates in bcf properly. It produces the 0
coordinate in the bcf correctly during bcftools annotate
, but bcftools view
then emits 4294967296 (ie. max uint32) when writing out the final vcf. This then snags on gsort
, which gives an "Unsorted positions" error.
This bug of bcftools is documented here:
- https://github.com/samtools/bcftools/issues/1753
- https://github.com/samtools/htslib/issues/1475
And is resolved by https://github.com/samtools/htslib/pull/1476.