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nikhil_joshi

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Nikhil Joshi

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  • Hello all, Can someone explain exactly how covariation works, in simple terms? I looked at the presentations in the dropbox folder from the link at the beginning of the comments, but I still don't understand. How exactly are context, cycle, rea…
  • Hello, I was looking over this documentation and I have a question about one of the examples above. The VCF line is this: chr1 877664 rs3828047 A G 3931.66 PASS [ANNOTATIONS] GT:AD:DP:GQ:PL 1/1:0,105:94:99:255,255,0 but the i…
  • Hi Geraldine, So I am looking at the lines, and they are indels. So it looks like where I went wrong is that I assumed when I gave the "-mode SNP" option to ApplyRecalibration, that it would only output SNPs. However, it seems that it outputs e…
  • Hi Geraldine, Thank you for your response. I apologize for the double posting, I thought I had posted in the wrong place the first time. So I understand your explanations, but I still have some results that I don't understand. You said that a …
  • So I have used the latest GATK best practices pipeline for variant detection on non-human organisms, but now I am trying to do it for human data. I downloaded the Broad bundle and I was able to run all of the steps up to and including ApplyRecalibr…
  • Hi Geraldine, So I must have copied a command that I tried somewhere in my command line... however, it seems to me that if JEXL has a problem with 30 vs. 30.0, that is a problem in JEXL. I'm a programmer and that doesn't seem like good coding. …
  • I think I found the problem and it is really strange.... probably a bug. And I am running the latest GATK, version v2.5-2-gf57256b. So when I run the command like this: java -Xmx2g -jar /share/apps/gatk/GenomeAnalysisTK.jar -T VariantFiltration…
  • So for example, here is the 2nd SNP line of the output vcf file after using "QD < 30.0" (as a test): chr8 79782250 . G A 571.25 PASS AC=5;AF=0.625;AN=8;BaseQRankSum=0.067;DP=21;FS=0.000;MLEAC=5;MLEAF=0.625;MQ=60.00;MQ0=0;MQRank…
  • Hi Geraldine, Thanks for your reply. So you are right... I mistakenly thought that MQRankSum occurred on every line, but it does not. However, the filtering still doesn't seem to be working.... I looked at the file and there is definitely a QD …