Hi all, I am currently trying to do some genotyping using some low-pass sequencing data on 13 1000GP samples. I am mostly interested in biallelic SNPS's. I have a variant calling pipeline built on GATK 4 (HaplotypeCaller) using the best practices, and another that uses Varscan2, and another using bcftools/samtools. The idea is to produce two call sets, before and after imputation (with BEAGLE) and check concordance with imputed 1000GP truth sets. Would any of you have suggestions on the best approach here? HaplotypeCaller may not be the best choice if there are only a few or one read is my thought. Any suggestions are appreciated! -Karl
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