missed variant calling for amplicon-based sequencing data using HaplotypeCaller
I am using GATK v3.7 HaplotypeCaller to genotype 2000 dbSNP variants, including SNPs and INDELs, from amplicon-based sequencing data.
--alleles is applied in HC, however, nearly 100 SNPs can not be successfully called in VCF file, either on simulation or real data (700~1000X).
UG is also tested in our pipeline, all the variants can be called, although realignment and BQSR is time consuming.
We are wondering the right command line for HC to call all our variants.
Or if UG is still the best way, can realignment and BQSR be skipped for our situation?