How to use HaplotypeCallerSpark from GATK 4 (beta 6) with Adam input files

ogirardotogirardot Member
edited October 2017 in Ask the GATK team

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

Issue · Github
by Sheila

Issue Number
2609
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
chandrans

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