I'm following this note in the GATK documentation: http://www.broadinstitute.org/gsa/wi...fied_Genotyper
However, I get no output when I run the UnifiedGenotyper tool with the -glm DINDEL option. If I run without the -glm DINDEL option, they work fine. There is no error or anything. The program just runs to completion and doesn't seem to report anything.
My command looks like this:
Has anyone used this successfully? If so, any tips? I know it's still a bit premature in its development, but I'd like to use it if possible.
However, I get no output when I run the UnifiedGenotyper tool with the -glm DINDEL option. If I run without the -glm DINDEL option, they work fine. There is no error or anything. The program just runs to completion and doesn't seem to report anything.
My command looks like this:
Code:
java -jar GenomeAnalysisTK.jar \ -l INFO \ -R human_g1k_v37.fasta \ -D dbsnp_130_b37.rod \ -T UnifiedGenotyper \ -baq CALCULATE_AS_NECESSARY \ -I recal.bam \ -o indels.raw.vcf \ -stand_call_conf 50.0 \ -stand_emit_conf 10.0 \ -A AlleleBalance \ -A DepthOfCoverage \ -A HaplotypeScore \ -glm DINDEL \ -nt 8 \ -L intervals.interval_list
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