- Logan UT
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- Logan UT
Hey Sheila and Geraldine, I finally figured it out! When aligning with bwa, I used the "-I" flag (bwa manual: "The input is in the Illumina 1.3+ read format (quality equals ASCII-64)"). I was not aware of the fact that Illumina …
Hey Sheila, considering that the Best Practices contain variant calling and call-set refinement, I have not been able to finish them (variant calling with the ploidy 3 option does not return any variants, whereas the diploid data work...) After in…
ok, here are two of the lines from the triploids when called as diploids. igv screenshots are attached (Quote) (Image) and (Quote) I noticed that igv gives base qualities for the two variants as -17 and -4, respectively. Negative phred scale…
ok, finally back... I tried to run the HaplotypeCaller (v3.5), without success. I used the same input data, with the following command (Quote) I tried a second run with the triploid individuals and -ploidy 3, without success. With the UnifiedGen…
ok, tried the same wth v3.5, with the same results. Will give the HaplotypeCaller a try.