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  • Hi Geraldine, Unfortunately, data privacy restrictions do not allow me to use/share our data. However, I'm sure that this effect will show up using publicly available data such as the 1000 Genomes samples, too. Cheers, Tim
  • Hi Shlee, Sorry for reposting and thanks for the extended answer. Cheers, Tim
  • Hi, Thanks for the great tutorial. I have a question: I'm trying to reproduce your tutorial results with the provided data. I ran into the problem that my resulting merged bam includes reads that are marked with the "XT" tag. However, a d…
  • Hello Geraldine, I'm sorry for opening this up again but I have to take my last comment back. The error did not (completely) disappear in gatk >=3.4. Although the error is decreasing, v3.4 still shows a difference of ~70.000 variants when the or…
  • Here's the chart:
  • Hello Geraldine and Sheila, I finally found the time to run all the tests. As I mentioned before the results of joint genotyping in v3.2 and v3.3 are biased based on the order of input files passed to GenotpeGVCFs. It affects the QD field of the ra…
  • Hi Sheila, As suggested I used SelectVariants to extract the variants of just one sample from two larger files and ran GenotypeConcordance on those two. The SelectVariants call was java -Xmx8g -jar /apps/gatk/3.5.0/GenomeAnalysisTK.jar \ -T SelectV…
  • Hi Sheila, Thanks for the reply. I will have a look at it tomorrow and compare the sub-sets as you suggested. I will let you know what the outcome is. Cheers, Tim BTW: I figured out that a site is "interesting" when it's unavailable/pre…
  • Hello Geraldine and Sheila, My apologies for the silence. I'm still running tests to make sure that it's not just our platform/system. But at the moment it seems that the order of the input gvcfs passed to GenotypeGVCFs affect the QD value of the re…
  • Hi Sheila, I ran this with GATK 3.3 but also 3.5 (no difference) java -jar GenomeAnalysisTK.jar -T GenotypeConcordance \ -R hs37d5.fa \ --comp comp.vcf \ --eval eval.vcf \ --out comp_vs_eval.out \ --printInterestingSites comp_vs_eval_discordance.o…
  • Hi Sheila, I tried to reproduce results from a sequencing provider but despite using the same parameters and thresholds I wasn't able to reproduce the same/similar VQS Lod values when training the INDEL/SNP models and therefore always filtered out …
  • Thanks again to both of you. Cheers, Tim
    in gvcf to vcf Comment by timk June 2016
  • Hi Sheila, thanks for the quick answer. Great. I wasn't aware that I can use VQSR also on single samples. But do I still use GenotypeGVCFs to create my raw vcf file from a gvcf? Cheers, Tim
    in gvcf to vcf Comment by timk May 2016