Hi, I am intending to do targeted resequencing for SNP variant analysis in different population by using MIP based sequencing using illumina platform. I have on hand, SNP containing fasta transcripts (generated previously), known SNP location and RefGenome i can download for Mouse as model. I am new to MIPgen tools. Can anyone suggest, 1) what would be the file format requirement for refGenome in MIPgen? 2) For capturing the exact location of the SNP location in my target sequence, in what format I need to provide the target region in MIPgen input? 3) If second answer is, genome coordinate in BED file, how do I take the coordinate of more than one lakh sequences? 4) I did not find the -regions_to_scan program in MIPgen tools collection, where will I find this program? I shall be highly grateful for your positive answer.
