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
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
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