Hi All,
For our alignment based wtss pipeline we have been using bwa for alignment and SNVMix to identify snps.
We're checking out the new versions of tophat to see if they will be good replacements for what we're doing now. Our problem is that our snp calling requires re-tuning since the mapping qualities are assigned differently in tophat (we see very few alignments with mapping quality above 40) than they are in bwa.
So, what is everyone out there using for snp calling on their tophat alignments?
-mpileup?
-gatk?
For our alignment based wtss pipeline we have been using bwa for alignment and SNVMix to identify snps.
We're checking out the new versions of tophat to see if they will be good replacements for what we're doing now. Our problem is that our snp calling requires re-tuning since the mapping qualities are assigned differently in tophat (we see very few alignments with mapping quality above 40) than they are in bwa.
So, what is everyone out there using for snp calling on their tophat alignments?
-mpileup?
-gatk?