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GTAK gives up sorting BAM file with strange quality scores
I have a problem processing a BAM file with GATK 3.4-46. This is my command:
java -Xmx3g -jar GenomeAnalysisTK.jar -l INFO -R resources/Homo_sapiens_assembly19.fasta -T UnifiedGenotyper -I /tmp/foo.bam -L Y -rf BadCigar -o /tmp/foo.vcf --output_mode EMIT_ALL_CONFIDENT_SITES
and I get an error:
ERROR MESSAGE: SAM/BAM/CRAM file [email protected]2734443 appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 63; please see the GATK --help documentation for options related to this error
I searched on the web and found that adding some more flags has helped some people to resolve the problem so I modified the command:
java -Xmx3g -jar GenomeAnalysisTK.jar -l INFO -R resources/Homo_sapiens_assembly19.fasta -T UnifiedGenotyper -I /tmp/foo.bam -L Y -rf BadCigar -o /tmp/foo.vcf --output_mode EMIT_ALL_CONFIDENT_SITES --fix_misencoded_quality_scores -fixMisencodedQuals
Now it fails in a different way:
ERROR 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
Any idea how to fix this?