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  • Hi Geraldine, maybe not definite in a scientific robust way. But after using the nct 6 option on my 8 core machine while running HC I got each time an error in different region of the genome en with different error types. That's why I blame these th…
  • I'm in between definite that the nct thread setting is the problem. Running HC on the Baserecalibrated and Leftaligned bam file with the nct 6 setting gave a new erro: Java.lang.NullPointerException after running for 58 minutes. Interesting becaus…
  • This time the HC produced after 60 hrs a vcf file. 12.3% reads were filtered out (HCMappingQualityFilter).
  • Hi Geraldine, I want to avoid that the indels that are private (only) to my genome and not part of the 1000G_phase1.indels.b37.vcf indel are to left out.But I did run in between (without waiting for mummy's ok!) the RTC and the IR with both argument…
  • Thanks again Geraldine. Looking at your name we could be 'zuiderburen'.
  • Re-running the HaplotypeCaller with the same specs in the area of the chromosomal interval (2:8478874 was the last variant noted) of original error did not replicate the error. I can therefore not send a snipped. I got a hunch that the nct setting …
  • Thanks again. I understand that these BD and BI tags are not used in further analysis of the Bam data such as variant calling etc.
  • The BadMateFilter was 4.3 % (I accidentally give the wrong number; sorry). I suppose that is much more acceptable; or is it still to high? After calling and calibrating the variants (UnifiedGenotyper/VariantRecalibrator/ApplyR.) i ReadBackPhased th…
  • Thanks! FixMateInformation improved the results of UnifiedGenotyper This time "only" 15 % BadMateFilter. Is further imporvement to be expected with Gatk Recalibrator/PrintReads?