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I have twice run UnifiedGenotyper and the resultant .vcf file contains only part of chromosome 20. I do not see what I am doing wrong. Neither do the other two people in the lab who have extensive experience with GATKcat
That's very odd, the log file seems to indicate that the run completed normally. Can you post the header of the vcf file?
Geraldine Van der Auwera, PhD
Human error. I had a -L 20 argument in the command that I did not want, but somehow got in (cut and paste?). That is so human and makes me feel so stupid. But it is just the way we are built. We humans see what we expect.. This is exactly why GATK exists, it never overlooks anything it is set to detect. So sorry to bother you and thanks for the response.
Hah, don't beat yourself up, it happens all the time
I'm glad your problem is resolved.