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.
Version 1.11 of bcftools in the
brentp/smoove:bdf809472b6adocker image doesn't support 0 coordinates in bcf properly. It produces the0coordinate in the bcf correctly duringbcftools annotate, butbcftools viewthen emits 4294967296 (ie. max uint32) when writing out the final vcf. This then snags ongsort, which gives an "Unsorted positions" error.This bug of bcftools is documented here:
And is resolved by https://github.com/samtools/htslib/pull/1476.