I have assemble paired-end RAD-seq data to be contigs. According to the 
practise "WGS/WES Mapping to Variant Calls - Version 1.0", the files will be 
manipulated by GATK. Unfortunately, GATK is extrimely time  consuming for large 
amount of small contigs. Can I connect the small contigs to be supercontig as 
reference with "NNNNNNNN" as saperator. If I use the supercontig as reference, 
is artificial linkage would affect SNP and Indel calling in population with low 
depth?  Or any suggestion? Thanks.
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