Hi, this is my first time posting on this forum. I'd like to know how I can get a list of indels and snps that two or more bam files share in common and what they do not share in common.
I came across this thread: http://seqanswers.com/forums/showthread.php?t=17644
I found a version of samtools for windows so I'm using that but I'm not entirely sure what to do from here. In the meantime I've been using integrated genome browser, integrated genome viewer, and sra tool kit to analyze this sort of stuff but I'm looking for a more "automated" way to do this. Igb and Igv are both really good for this but I still have to manually go through both bam files in the same window and make my own analysis of what is similar and different between the sequence reads.
I'm sorry if any of this sounds confusing, like I said I'm completely new to this and I am just now teaching myself how to do this. Any advice or suggestions would be greatly appreciated
For the record I'm running on windows 7 64bit os
I came across this thread: http://seqanswers.com/forums/showthread.php?t=17644
I found a version of samtools for windows so I'm using that but I'm not entirely sure what to do from here. In the meantime I've been using integrated genome browser, integrated genome viewer, and sra tool kit to analyze this sort of stuff but I'm looking for a more "automated" way to do this. Igb and Igv are both really good for this but I still have to manually go through both bam files in the same window and make my own analysis of what is similar and different between the sequence reads.
I'm sorry if any of this sounds confusing, like I said I'm completely new to this and I am just now teaching myself how to do this. Any advice or suggestions would be greatly appreciated
For the record I'm running on windows 7 64bit os