Hi
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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