Finding SNPs

[Big_Cheese]

hi, i am new to bioinformatics, but im trying to find mutations in the mouse genome. To do that I use BWA to align all the reads from Solexa Sequencing to a reference Sequence and then export them.

My Question is whats the best tool to compare my consensus Sequences and filter out known SNPs, so I can find out what changes are actually mutations?
I got the reference Sequence of the Mouse, a Control Group Sequence and 3 Mutated Sequences and would like to Compare them.

Another thing is that I am currently using UGENE with the BWA tool.
I use the SAMtools for the consensus sequence, which works quite good.
For example if a C changes to a T/C(which means in 50% of the reads there is a T, in the other 50% der is a C) it puts another Letter there(I think R) which is exactly what I need. But sometimes that doesnt seem to work. I cant explain why but in some cases the program puts a C in the Consensus line although it is obvious that it's a C/T. I couldnt find any options and I would like to know what I can do to fix that

[adaptivegenome]

GATK works well for SNP calls and allows you to supply a list of known SNPs.

[Big_Cheese]

any ideas how I could do that with windows 64 bit?

[adaptivegenome]

GATK is written in Java, I imagine that any machine with a JVM should be able to run it just fine.

But I have not used Windows in 10 years (I use MacOS and Linux), you might ask others on the board if they have any issues.

[shyam_la]

There are no issues with running GATK on windows. I would suggest you install 64 bit JRE on your machine, so that you can use the full physical memory available to you..

[adaptivegenome]

GATK Is your best option...

[Big_Cheese]

ok thank you,
I was confused because they say on their homepage that GATK doesnt support for windows and I didnt manage to get SAMTools or Pysam running on windows either,
but then again I am not very experienced with programming in general

"The GATK was designed and is intended for use on Linux (and other POSIX compatible) platforms. We do not currently support running it on a Windows platform. "

[adaptivegenome]

ok thank you,
I was confused because they say on their homepage that GATK doesnt support for windows and I didnt manage to get SAMTools or Pysam running on windows either,
but then again I am not very experienced with programming in general

"The GATK was designed and is intended for use on Linux (and other POSIX compatible) platforms. We do not currently support running it on a Windows platform. "

Yes, but Java is usually cross-platform. Samtools is written in C and can sometimes be a little more tricky to compile for different platforms although I remember several threads on SEQanswers that address this.

Any reason you do not want to work with Linux?

[Big_Cheese]

well I am working on this relatively strong computer for sequencing(25Gig RAM, 8 cores) and its operating system is windows and since I do not have much experience with linux I was kinda hoping that I would find an easy way to do it in Windows.
Well anyway I guess I will have to dualboot or get some program that simulates Linux

[adaptivegenome]

You could use cygwin but I would recommend just dual booting. There are so many other commands/features that make Linux an easier platform for analyzing genomes.