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  • Hi Sheila, These values were passed the filter --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" Also, I have another question. Why Most of snps which had high GQ, but th…
    in GQ Comment by wendy February 2017
  • Hi Geraldine, It is true that these calls made from diploid data. However. I'm not sure what you mean about " it makes sense to me that whenever you see AF diverge strongly from the value that matches ideal ploidy, we will be less confident t…
    in GQ Comment by wendy December 2016
  • Hi Geraldine, This is the example of record showing this trend. We could find that the average of GQ increase as AF increase. However, in my opinion, when snps got low AF they also should get high GQ. Because that means it is easy to confirm the ge…
    in GQ Comment by wendy December 2016
  • No, Shelia post a Github link above my question. I though it is about the function of "raw PL". isn't it? I have downloaded the source code but I cannot find the function
    in PL Comment by wendy March 2016
  • HI, Should I need to link the Github? Because I cannot link it successfully. Wendy
    in PL Comment by wendy March 2016
  • yes, I am familiar with java, but there are too many function that I cannot find which I should modify. Thank you! Wendy
    in PL Comment by wendy March 2016
  • HI Can you tell me which function should I change? Thank you! Wendy
    in PL Comment by wendy March 2016
  • Here is my commend line! java -Xmx4g -cp ${classpath} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -cp ${classpath} \ -gatk ${…
  • Dear Sheila and Geraldine Thanks your help :) Wendy
  • Hi Sheila 1. Why it didn't have DP in this position? 2.when DP=".", why it stills give a Genotype? Wendy
  • HI! I used GATK-3.4-46 to run "hard filtering" GenomeAnalysisTK.jar -T SelectVariants -R ../human_g1k_v37_decoy.fasta -V output_100.vcf -selectType SNP -o raw_snp_new.vcf GenomeAnalysisTK.jar -T VariantFiltration -R ../human_g1k_v37_decoy.…
  • Hi Sheila, Thanks for your help!! :) Wendy
  • Hi Sheila, Thank you very much!! But, I have another question, before I merged the gVCF file they include a lot of SNPs. However,after I used "GenotypeGVCFs" to merge them, all of them become indels. Is it normal? (In attach file,right si…
  • Hi Sheila, So I need to run "hard filters to a call set" after GenotypeGVCFs right? Thanks,Wendy
  • Hi Sheila, my command: /pkg/java/jre1.8.0/bin/java -jar ../GATK_3.4-46/GenomeAnalysisTK.jar -T VariantRecalibrator -R human_g1k_v37_decoy.fasta -input output_40.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.vcf…
  • Hi Geraldine , Many thanks for your answer!
  • Hi all, After I use hard filtering.I got two data(filtered_snps.vcf and filtered_indels.vcf ). Should I merge these two data for the following steps? Thanks for help! Wendy
  • Hi Geraldine and Sheila, Many thanks for your answer!
  • (Quote) HI, I have whole genome data,after re-run the pipeline without using the -L argument and add in the 1000 Genomes data. 1.About "Once you have the results......",what is the "result" means? 2. Which steps should I use Sel…
  • hmmmmmm.....actually, I still cannot understand your reply. Could you explain that in easier way?? My question is... My NGS data had been use " -L argument " to choose the intervals of 100 gene,and I want to add 1000 Genome whole exome dat…
  • Hi Geraldine,I've tried running with the default tranches (version 2.7 and 3.1). But I still got the same weird results (please see attached). And why the ti/tv is lower than expected? Any ideas would be welcome. Thanks,Wendy