search

SouthGreenPlatform / arcad-hts

Scripts for the analysis of high-throughput sequencing data from the ARCAD project.
http://www.arcad-project.org/
GNU General Public License v3.0
0 stars 1 forks source link

Make an option in for -fixMisencodedQuals in arcad_hts_6_bamRealignerRecalibrate.pl #13

Closed nrode closed 9 years ago

nrode commented 9 years ago

It seems that by default, the script assumes that there is a quality mispecification and use the flag -fixMisencodedQuals when calling GATK -T RealignerTargetCreator, which produces the following error message: MESSAGE: Bad input: while fixing mis-encoded base qualities we encountered a read that was correctly encoded; we cannot handle such a mixture of reads so unfortunately the BAM must be fixed with some other tool Would it be possible to make it an optional argument?

gsarah commented 9 years ago

Done.

I added a -fixMisencodedQuals in arcad_hts_6_bamRealignerRecalibrate.pl