I am wondering how people generally go about local realignment around indels in their workflow?
The most popular programs seem to be SRMA and GATK - does anyone use anything else?
In my initial tests this seems to be a VERY time-consuming step when compared to the initial alignment step. Does anyone employ methods of speeding up the process? For example, only realigning within exonic coordinates OR perhaps performing variant calling first and then using the coordinates from the VCF to restrict the areas where realignment is performed?
I am trying to set up a SNP/Indel workflow and realignment seems to slow it to the the point where it becomes useless for anything but small numbers of samples. I tested on a single chromosome and it took 4.5 hours. Alignment and variant calling without realignment only took about 1.5 hours for the whole genome!
Thanks in advance!