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lalir

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lalir
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  • Hello @Geraldine_VdAuwera and @Sheila I just have a follow up question for this thread. If I am using the -genelist argument, will the per gene statistics be based on the intervals specified in the -L argument? For instance, will the per gene statis…
  • Sure, here is the example I was talking about: @Sheila ####SNP in individual sample#### chr22 38509628 rs141777179 C T 86 PASS AF=0.393443;AO=24;DP=61;FAO=24;FDP=61;FR=.;FRO=37;FSAF=1;FSAR=23;FSRF=16;FSRR=21;FWDB=-0…
  • Hi @Geraldine_VdAuwera, I just need some clarification: Should I use the intersect file as the comp or eval with GenotypeConcordance? Also, I realized that the references sequence I was using in the -R argument was different than the reference seque…
  • Hi @Geraldine_VdAuwera‌ I realized this and ran CombineVariants and used SelectVariants to select out the calls that intersected between the two files. Should I use this file in GenotypeConcordance?
  • Hi @Geraldine_VdAuwera Thanks for your reply. I have posted what you requested below: java -jar GenomeAnalysisTK.jar \-T GenotypeConcordance \-R ucsc.hg19.fasta \--eval input1.vcf \--comp input2.vcf \-o results.vcf These are from the input1.vcf …
  • Hi Sheila, Thanks for you help. I do not believe my VCF files contain all the necessary annotations so I will have use VariantAnnotator first. Also, I noticed the article mentioned that callsets containing at least 30 samples are recommended for bes…
  • Thank you, Yes, I suppose that the specificy/sensitivity is dependent on the variant caller used. It's called variant caller 4.2 and is integrated into the Ion proton system.