Hello,
I used UnifiedGenotyper and HaplotypeCaller on my sample to get out INDELS and SNPS. There is a 147bp deletion in one of the genes(working with yeast genome)(see attached file). But this deletion is not reported by UnifiedGenotyper and HaplotypeCaller. Since I am working with yeast genome(which is comparatively very small compared to human genome), I am only interested in INDELS ranging from 150bp-200bp maximum. Is there a way by changing parameters that this can happen. I have read some of the previous questions about how haplotypecaller is unable to call large INDELS(in kb's), but I guess in my case INDELS max I am looking for is 200bp. Can this be achieved??
Also UnifiedGenotyper has an option to provide ploidy level. I could not locate that option in HaplotypeCaller. Any way to have that on HaplotypeCaller ? I ask you this because the yeast genome samples I work with are eseentially haploid.
NOTE: My sample is paired end data with 100bp reads
Hope to hear from you soon
Regards Varun