Undercall heterozygous SNP's in draft assemblies
A draft NGS genome assembly generated using ALLPATHS-LG is being used as a reference for SNP calling using GATK. Does GATK undercall heterozygous SNP's in certain regions(repeat regions, ends of scaffolds etc) of such draft assemblies?
Alignments at ends of contigs are listed as an artifact in this website. (http://pathogenomics.bham.ac.uk/blog/2013/01/sequencing-data-i-want-the-truth-you-cant-handle-the-truth/).
Could you please let me know the set of tests that need to be run to identify such artifacts? Does GATK have an option to exclude such regions from being used for SNP calling?