We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Error in GatherBQSRReports
starting from WES pair-end data...
in the BaseRecalibrator step I used as interval these regions/chr:
chr1-22, chrX, chrY, chrM, alternative contings and HLA contings. In the case of HLAname I added at the end of the name ":1+"
Next , in the GatherBQSRReports step I saw in the log file this "error":
### START LOG FILE
05:24:49.607 INFO GatherBQSRReports - Done initializing engine
05:24:54.887 INFO RecalibrationReport - Missing read group(s): /home/manolis/GATK4/IlluminaExomePairEnd/4.BAM/processing/15_1143_030_recaldata.csv
05:24:54.916 INFO RecalibrationReport - A00125.27
05:24:54.917 INFO RecalibrationReport - Missing read group(s): /home/manolis/GATK4/IlluminaExomePairEnd/4.BAM/processing/15_1143_031_recaldata.csv
05:24:54.917 INFO RecalibrationReport - A00125.27
05:24:54.972 INFO RecalibrationReport - Missing read group(s): /home/manolis/GATK4/IlluminaExomePairEnd/4.BAM/processing/15_1143_811_recaldata.csv
05:24:54.972 INFO RecalibrationReport - A00125.27
05:24:59.650 INFO GatherBQSRReports - Shutting down engine
[February 20, 2018 5:24:59 AM CET] org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports done. Elapsed time: 0.17 minutes.
### END LOG FILE
15_1143 = Sample ID; 030, 031... 811 custom chr/conting ID
[ "," is intended as "\n"]
custom chr/conting ID: 1-25 = chr1-22,X,Y,M (example: chr1 , ... , chrX , chrY , chrM)
custom chr/conting ID: 26-286 = Alternative contings (example: chr1_KI270762v1_al t, chr1_KI270766v1_al, ...)
custom chr/conting ID: 287-811= HLA contings (example: HLA-A01:01:01:01:1+ , HLA-A01:01:01:02N:1+)
custom chr/conting ID reported "Missing read group(s)"... example
ID 30: chr1_GL383518v1_alt
ID 31: chr1_GL383519v1_alt
ID 811: HLA-DRB1*16:02:01:1+
"Missing read group(s)" progress ID
... ... ...
The ID not reported in the log file are ok... I think All downstream steps, until the HaplotypeCaller step work. I have not get tried the steps downstream of HaplotypeCaller...
This "Missing read group(s) error is repeated 563 times. The number of chr/contings in the interval list is 811.
All the best