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Hi. I was hoping you could help track down the source of this error. I haven't seen this exact error anywhere here in the forum. I am trying to run unified genotyper on 48 bam files at once. Each bam file has been aligned using bwa and processed through the best practices as mentioned on the website. They all pass validation with no error (I had to run picard tools, cleanSamFile and fixMateInformation, along with removing one read from a single file). The data is targeted sequencing. I am running GATKLite 2.3-5-gd738181.
The error message is:
Somehow the requested coordinate is not covered by the read. Alignment 189665677 | 48M103S
The command line I am using is:
java -Xmx4g -jar pathToGATK.jar -R standardRefFileHG37 -I (48 bam files) -o OutputFile.vcf -nt 4 -nct 4 -T UnifiedGenotyper --dbsnp standardRef -glm Both -metrics metric.file -debug_file debug.txt -A DepthOfCoverage -A AlleleBalance
Is there any way to see if it is a particular bam file that is causing the error? In the error message, what Alignment is it referring to? I am doing the processing on a machine that is not connected to the internet so it is harder for me to cut/copy paste information to here. Is there anything else that you would need to help me track down the source of this error?
In the meantime I am going to try to run it with a .bed file of targeted areas to see if that helps. Should I also try to process each file individually? Thank you for your input.