In order to discover the SNPs among my samples, I have used MPileup as a tool from SAM tools. However when I run bcf tools view to see the file, I see a tabular file with only 26 comments. When I got this problem more than once I checked the MPileup file output I saw that log file shows some 28,000 lines with the "The sequence "TR1|c0_g5_i1" not found" for all the lines. I am just wondering what is happening wrong?? But MPileup bcf format file is 2.6 GB.
Could anyone please help me find a possible source of error?
Any help is appreciated