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giab-NA12878 truth_small_variants.vcf.gz header issues #1566
Two issues found in this validation VCF file: they use
For the first error message, failing on Type=String for phase set PS is going to be common.
I was thinking of creating an issue to fix the second error message (tribble complaining about BCF), but that is actually an issue with Hadoop-BAM HadoopGenomics/Hadoop-BAM#132
The BAD_PS phase set for GT VCF FORMAT field with Number=-1 cardinality restriction header line comes from ADAM. This is the actionable issue here.
Grr... looks like we need to switch on countType, if it is