We are focusing on 3000 known SNPs.
Instead of genotype these SNPs from array or taqman, we use PCR to enrich these SNPs, and get them sequenced on HiSeq.
We found genotype these 3000 SNPs cost lots of time.
We split the 3000 SNPs into two categories,
1000 of them were called by GATK UnifiedGenotyper, while the others were genotyped by HaplotypeCaller, using --genotyping_mode GENOTYPE_GIVEN_ALLELES --alleles $vcf --output_mode EMIT_ALL_SITES?
However, it take ~18h to process all these SNPs. Is there any other methods to genotype these SNPs?