I want to know what values should be used for these parameters on pacbio sequel data (these are whole genome data from a haploid fungus). For example on the illumina data I use the values below:

For Base calling

$   HaplotypeCaller -R Reference.fa -I sorted_marked.bam -ploidy 1 -ERC GVCF   --variant_index_type LINEAR --variant_index_parameter 128000 -stand_emit_conf 10 -stand_call_conf 30 -o raw_gVCF.vcf

For SNP filtration

$    VariantFiltration -R reference.fa -V raw-snps.vcf --filterExpression 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0' --filterName “my_snp_filter” -o filtered_snps.vcf

For Indel Filtration

$   VariantFiltration -R reference.fa -V raw-indel.vcf --filterExpression 'QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0' --filterName “my_indel_filter” -o filtered_indels.vcf

I have no idea about the values that should be used for these parameters on pacbio sequel data. Or do I use the same values?

these are subreads generated by sequel