Dear GATK Team,
I was trying to use joint calling by GATK, first I aligned the RNA-Seq reads to a genome reference using HISAT, and the overall alignment rate was over 70% with over 50% read pairs mapping concordantly only once. Then I marked the duplicates using Picard. The command I used for individual libraries is: java -jar /path/to/GenomeAnalysisTK.jar -T HaplotypeCaller -R -I --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -o
Could you provide some guidance to try figuring out what could be the issue here?