Terry Jones
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Latest activity by Terry Jones-
Terry Jones commented,
OK, looks like I have this fixed. If the @RG line contains a SM:name tag, the original error does not occur. Maybe the error messages above could be changed to say what sample names are found or to...
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Terry Jones commented,
BTW, I also tried using --sample-name RG_NAME (where RG_NAME is the name of the single read group in the BAM file). I get the same (second, above) error, telling me that the sample name doesn't exi...
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Terry Jones created a post,
HaplotypeCaller complains (in 2 different ways) about sample-name
I'm using GATK v4.1.4.1 running this: gatk --java-options -Xmx4g HaplotypeCaller -R ref.fasta -I input.bam -O output.vcf.gz I get an error: A USER ERROR has occurred: Argument emit-ref-confidence h...