Soap2 Alignment Output For Snp Calling
I'm using SOAP2 aligner to map some short reads to Glycine max v1.01 reference genome. The reads are paired-end soybean reads from Lam et al. 2010. SOAP2 produces two output files: the paired-end and single-end mapping. The paired-end one is significantly larger in size.
My question is, for the purpose of SNP calling (I will try some variant caller tools), which mapping result should I use? The paired-end, single-end, or both? If I have to use both, could I simply concatenate those two output files?
Any suggestion is appreciated, since I'm new to bioinformatics. Thanks.
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