IndelRealigner no initialization
Posted in Ask the GATK team | Last updated on 2012-09-25 19:32:13

Comments (10)

I got this when I ran the IndelRealigner. The output bam is empty.

INFO  15:19:35,568 TraversalEngine - Total runtime 0.00 secs, 0.00 min, 0.00 hours
INFO  15:19:36,910 GATKRunReport - Uploaded run statistics report to AWS S3

It didn't initialize. The sample is aligned to specific region of the genome and I did use -L option. For whole genome alignment of the same sample, I don't have any problems. Do you know why?

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