Join GitHub today
GitHub is home to over 28 million developers working together to host and review code, manage projects, and build software together.Sign up
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
referenced this issue
Aug 22, 2017
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