Entering edit mode
5.4 years ago
Zeason
▴
10
hi guys,do you ever use mutmap pipeline to do some practice? recently, i just do some practice with the data the author used in their journal. i do very step as the protocol told me to do , but i always got this wrong: Your base quality format appears a illumina type, but the job will be processed with sanger type . To change it use -calltype option. it came up in the Coval refine snp step. i dont kown how to fix it , it really bother me deeply. thanks very much!
I assume you are referring to this pipeline?
The quality score encoding for fastq files went through a few iterations over the years (you can read about the types in this article). The data you are using may have been encoded using older
Illuminaencoding (I or J type in the WP article) where as the standard now has become Sanger (phread+33) encoding. You may have to use-calltype illumina(look up the specific option in the pipeline manual) to avoid getting that warning.the thing is very weird , i download the data as this protocol recommended to do my practice. And i also change the specific option as the protocol told me to do, but it still get this wrong. It really confused me.