best way of filtering out common SNPs in the GATK outputted VCF file
In my PiCard/GATK pipeline, I already include the 1000G_gold_standard and dbsnp files in my VQSR step, I am wondering if I should further filter the final vcf files. The two files I use are...
View ArticlePicking a VQSR tranche for indels
Hi, Given that there's no tranche plot generated for indels using VariantRecalibrator, how do we assess which tranche to pick for the next step, ApplyRecalibration? On SNP mode, I'm using tranche plots...
View ArticleVQSR error: NaN LOD value assigned
INFO 17:05:50,124 GenomeAnalysisEngine - Preparing for traversal INFO 17:05:50,144 GenomeAnalysisEngine - Done preparing for traversal INFO 17:05:50,144 ProgressMeter - [INITIALIZATION COMPLETE;...
View ArticleVQSR plots
hi i run VQSR on the vcf file generated by unified genotyper and filtered PASS 63412 out of 86840 (files with snps and indels). as i run unified genotyper with -glm BOTH command. i have two questions...
View ArticleMills reference for indel VQSR
Hi all -- This should be a simple problem -- I cannot find a valid version of the Mills indel reference in the resource bundle, or anywhere else online! All versions of the reference VCF are stripped...
View ArticleVQSR on single exome
hi, Geraldine, Thanks for the webinar! You mentioned that VQSR isn't necessary for a single exome. But would there be any drawback to run it on a single exome? I see that it helps to set up the PASS...
View ArticleVQSR bundle based on b37 and hg19
Hi, Sorry to bother you guys. Just a few quick questions: 1) I'm attempting to download the bundles for VQSR and I noticed that they are for b37 or hg19. If I performed my initial assemblies and later...
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VQSR on ~500 genomes
Hi, I am working on VQSR step (using GATK 2.8.1) on variants which have been called by UG from ~500 whole genomes of cattle . I run VariantRecalibrator as following: ${JAVA}...
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How should I interpret Phred-scaled Quality Scores?
You may have noticed that a lot of the scores that are output by the GATK are in Phred scale. The Phred scale was originally used to represent base quality scores emitted by the Phred program in the...
View ArticleBug in VariantRecalibrator
Hi there, So for the SNV model in VariantRecalibrator, I was using QD, MQRankSum, ReadPosRankSum, FS for a little while and then decided to add MQ back in since I saw that BP was updated recently and...
View ArticleVQSR on exome of small specific population
Hello, I've asked this question at the workshop in Brussels, and I would like to post it here: I'm working on an exome analysis on trio. I would like to run VQSR of filteration on the data. since this...
View ArticleVQSR VariantRecalibrator Rplot
java -jar -Djava.io.tmpdir=temp/ -Xmx4g GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -T VariantRecalibrator -R hg19.fa -input NA19240.raw.SNPs.vcf...
View ArticleVQSR filter
Hi, I have exome sequencing data on 90 samples, and my lab uses the VQSR filter to remove low quality variants. I was wondering if I should also perform a genotype-level filter by DP/GQ post this VQSR...
View ArticleIs BQSR necessary for de novo mutation calling?
Hi there, I have been using GATK to identify variants recently. I saw that BQSR is highly recommended. But I don’t know whether it is still needed for de novo mutation calling. For example, I want to...
View ArticleVQSR
Hi, I am working on non-human species data and i have used VQSR in the analysis pipeline as shown below: If VQSR is performed, should we still consider filtering the variants on basequality and mapping...
View ArticleMissing QD tags at some positions
Hey there, How can it be possible that some of my snps or indels calls miss the QD tag? I'm doing the recommended workflow and I've tested if for both RNAseq (hard filters complains, that's how I saw...
View ArticleDetecting SNV in human populations
Hello Geraldine, First thank you a lot for your amazing work on this forum. My project deals with discovering rare population-specific variants in human exomes, and I would like to know how the VQSR...
View ArticleVariant Recalibration on related Samples
Hi GATK team, our lab has a never ending discussion about running VQSR on related samples or having to exclude them. And i guess we need your help to settle this. We have a multisample call (UG) run on...
View ArticleRandom Forests VQSR
Hi there, I hope I'm not being too forward here, but I was wondering if your group was still looking into implementing a RF model for VQSR (in particular I was hoping that it would help with smaller...
View ArticleStack trace error while running VQSR
I'm trying to run VQSR on a vcf I just called with HaplotypeCaller. Here is my command: java -Xmx32g -jar /Commands/GATK/GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R /Reference/ucsc.hg19.fasta \...
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