[Samtools-help] small contigs connected to be superreference

[郭梁 <zs...@16...>]

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.