Entering edit mode
5.5 years ago
phongphak.06
▴
10
Hi, I'm now reanalyzing WGS data of some virus sequenced by 454. I want to identify SNPs using LoFreq. However, the indel realignment method of GATK is not working for 454 data. Is there any suggestion about the tools or methods that can replace this?
Why it is not working? Does it throw any error message?
Have a look at ICC.
I got a message like 100% of my reads failing Platform454Filter. So when I take a look at GATK documentation I found this comment:
Because reads produced from the 454 technology inherently contain false indels, the realigner will not work with them (or with reads from similar technologies)