I looked at some links of GATK on pacbio data but I can not understand that they are the parameters that must be used on
-variant_index_parameter , -stand_emit_conf , -stand_call_conf during the base calling by haplotypecaller.
Also for VariantFiltration of SNP and Indel
-filterExpression 'QD || FS || MQ || HaplotypeScore || MappingQualityRankSum || ReadPosRankSum
Could you give me an example of the base call on pacbio data with the values of these parameters.