Hi,
it seems that GatkReads can read SAM/BAM/CRAM files and Adam files.
But when I try to use HaplotypeCallerSpark with adam parquet files it fails because of some dictionnary validation ?
Here's the command line I use (same command line that I use with SAM files, I just changed the input path) :
./gatk-4.beta.6/gatk-launch HaplotypeCallerSpark \
--sparkMaster spark://<my spark master> \
--input "input.adam" \
--output output.vcf \
--reference /data/hg19/hg19.2bit \
-- --sparkRunner SPARK --driver-memory 10G --executor-memory 10G