I am playing around with two vcf files I generated with GATKv3.7. Both were generated with the parameters
-G Standard -G AS_Standard, but one was generated in GGA mode from the sites of the other. That GGA vcf has some AS_Standard values missing.
##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
But for some nonspecific number of variants they are annotated
AS_MQ; with no float given. I noticed this from an attempted merge of their shared variants using bcftools.
Not ready for type : AS_MQ at 12133603 was the exact error.
I was able to merge after sed replacing any value or AS_MQ; with AS_MQ=.; but I was wondering if there was any tool/command that could have done this for me and for any potentially wrong/missing value in a vcf format aware manner? I can build in a manual check for that AS_MQ fix, but I am trying to "fool proof" it in case it ever happens in another annotation.