hello everobody , in my project , i have to detect the variants (SNP and indels) in my genome sequences. for that , i create a pileup and i use varscan as tools. to create the pileup data , i tried two tools : 1- MPileup multi-way pileup of variants 2- Generate pileup from BAM dataset when i did the varscan , the results were different. in the first case , it detects 967 SNP , and in the second 1142 SNP. The additional bases that are detected were really present. someone can tell me what is the difference please! best of regards! Racha
The two tools are different algorithms, so the same exact calls are not expected. See the tool's manuals for the details.
Both tools have many settings that determine which SNPs are reported. From what you state, it sounds as if the settings for MPileup were set to be more stringent than you would prefer. Perhaps test out different options with both tools, compare, and then decide which to use/optimal settings.
For reference, Galaxy tutorials: https://galaxyproject.org/learn/
Thanks, Jen, Galaxy team