I'm working with 100bp Illumina Paired end, and I have been following the GATK best practices v3.
First, I mapped with BWA.
In INDEL mode, UnifiedGenotyper returns nothing.
Second, stampy.
In INDEL mode, only one large indel, and it was a false positive.
When doing base recalibration I did not have a list of known sites. Could this be such a significant problem that UG would return nothing?
First, I mapped with BWA.
In INDEL mode, UnifiedGenotyper returns nothing.
Second, stampy.
In INDEL mode, only one large indel, and it was a false positive.
When doing base recalibration I did not have a list of known sites. Could this be such a significant problem that UG would return nothing?