The MAPHiTS pipeline allows the detection of single nucleotide polymorphisms (SNPs) and small insertion/deletions (indels) by comparing high-throughput Illumina short-reads (GAIIx or HighSeq) with a reference sequence from the same or a different species. This pipeline is based on public softwares (BWA, Bowtie, SAMtools, VarScan and Tablet) and homemade tools. In particular, we developed tools to filter out short-reads of low quality and to prepare the mapping and SNP calling. We also developed tools to filter out the called SNPs according to genome coverage, allele frequency, pValue, and SNP positions in the read. Finally, we develop tools to parallelize all needed computation on a computer cluster. Most analysis runs in few hours on our 700 cores computer cluster.