I am beginner in the field of NGS. I want to do SNPcalling and using GATK as well as Samtools, but currently GATK not supporting latest version of hg38 . I am using the Illumina seq data and Iontorrent PGM datasets. Can you suggest better tools for SNPcalling other than GATK and Samtools ?
It could be really nice, if you can provide your review and feed back or opinion as well as scientific citations about your used tools for SNPcalling?