I am working with a genome that hasn't been sequenced but we do have some de novo assembled contigs to use as a "reference genome" for mapping reads against. I have ~91,000 contigs in this "reference genome". After mapping reads to this "reference genome" I want to then run variant calling using mpileup. The issue that I see is that my pileup file doesn't contain the SNP information for all 91,000 contigs contained in my SAM file. Can anyone tell me why this might be happening? Much of the data from the SAM file just doesn't make it into the pileup file and I don't know if it is because I have so many contigs in my "reference genome". Any help would be greatly appreciated.
Thanks Patricia Klein Associate Professor Institute for Plant Genomics and Biotechnology and Department of Horticulture TAMU2123 Texas AgriLife Research Texas A&M University College Station, TX 77843-2123
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