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  • I uploaded under UGErrorV2.tgz, but please ignore this for now. I want to try one more thing before I bother you guys : ).
  • Well, would you like the same test set I had sent you before but without the bad cigar strings? The cigar strings for these guys are now flawless (no "0M" in the cigar string) so it should be easy to isolate the error.
  • OK, I think I've got a fair idea on how the bug is occurring. When I split up my cohort of ~118 BAMs into 59 and 59 BAMs and run the genotyper twice in parallel, the error seems to be gone. When I try to genotype the whole cohort in total, I get t…
  • Running with -rf BadCigar did not actually work for me. I tried reprocessing my .bam's with a newer version of Picard and those too did not genotype correctly (the only problem with SAM validation I had was a missing NM tag which I thought was opti…
  • Hey guys, I gave the nightly build from each of the past four or five days with the test chromosomes and still no dice. Should I keep trying every day or wait for the next official release? Thanks!
  • Thank you very much! Look into things on our end as well so we don't throw any odd CIGARS into the pipeline from now on. Thank you for the phenomenal work! Our thoughts are with you and the rest of the Boston community.
  • Hi Geraldine, just pinging you on how the UG debug is going. Any progress or anything I can help with?
  • i) The reference I've been using is hs37d5 which I can upload, but I'm pretty sure I downloaded it from a Broad server, so I bet you have a copy on hand. The .bam header might imply that this isn't the reference, but I can assure you it is. ii) Th…
  • -R hs37d5.fa -T UnifiedGenotyper -L 21:28560000-28700000 -glm BOTH -nt 4 -ped myPed.ped -I BAMSForGenotyping.list -o 21.raw_MasterGenotypes.vcf
  • I've uploaded the bug report (under AJB_UG_error.tar.gz). Thanks for the assistance and hopefully it is an easy fix!
  • Sorry, that formatting got messed up, not intentional!
  • Same problem: ERROR ------------------------------------------------------------------------------------------ ERROR stack trace java.lang.IllegalArgumentException: Duplicate allele added to VariantContext: T at org.broadinstitute.variant.var…
  • I'm giving it a shot now, I'll post the results as soon as I get them. Thanks!
  • I generated it using the RealignTargetCreator passing minimal inputs (input bam, reference). The .intervals file looks like: ... x:y \n x:y'-z' ... Where y, y', and z' are all integers. x can be an integer, or X/Y/MT. Separation is newline.
  • File names changed, but here it is: INFO 10:33:14,849 HelpFormatter - ---------------------------------------------------------------------------------INFO 10:33:14,853 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-11-g13c0244, Compiled…
  • Excellent! Thank you very much for the speedy reply. But what is the syntax option to do so?