VQSR, VQSLOD, and indels
Hi Mark, Eric - First, I wanted to thank you guys for providing advice with respect to running VQSR. I am already sold and a huge fan of the method :-). I was wondering if either of you could comment...
View ArticleVariantRecalibrator plot?
HI again! Could you please help me to generate the first plot in the attached file which refers to VariantRecalibrator? In other words, is this plot generated at the same time as...
View ArticleVQSR for small exome data sets
Hi, I'm working with trios and small-pedigrees (up to six individuals). The VQSR section of the 'best practice' document states that 'in order to achieve the best exome results one needs an exome...
View ArticleVQSR and sex chromosomes
Hi, Maybe I have not been able to find some obvious piece of documentation, but I am searching for best practices in using VQSR with sex chromosomes (especially X)? I am trying to do variant calling on...
View ArticleHow to use the VQSR -tranche argument
How should I use the VQSR -tranche argument? From the tutorial I get that I should specify the list of doubles like this: -tranche [100.0, 99.9, 99.0, 90.0]...
View ArticleAny way to get past "Clustering with this few variants and these annotations...
Hi team, thanks for a great job developing this software! I am planning to use the GATK in a class as a demo of how to do SNP detection and the VQSR in a non-model organism, but due to time constraints...
View ArticleVQSR
Hi, I am working on dog genome and trying to use VQSR on my data. Here is the command i have used: java -Xmx4G -jar GenomeAnalysisTK.jar -R genome.fa -T VariantRecalibrator -input GATK-snp.vcf...
View ArticleVQSR on GENOTYPE_GIVEN_ALLELES mode
When using GENOTYPE_GIVEN_ALLELES with HaplotypeCaller, which uses EMIT_ALL_SITES and so has many calls where the entire cohort is nonvariant, do these reference only sites have to be filtered out...
View ArticleERROR stack trace ; Unable to retrieve result ; A GATK RUNTIME ERROR has...
Hi, Thanks very much for your answers for my previous questions. It seems that I encountered another difficulties when I run the QVSR steps because some ERROR information was spotted on the screen....
View Articlewhat does this mean in VQSR output vcf files?
I have the following entries in my vcf files output from VQSR. What does the "VQSRTrancheINDEL99.00to99.90" string mean? did they fail the recalibration? PASS VQSRTrancheINDEL99.00to99.90...
View Article(howto) Recalibrate variant quality scores = run VQSR
Objective Recalibrate variant quality scores and produce a callset filtered for the desired levels of sensitivity and specificity. Prerequisites TBD Caveats This document provides a typical usage...
View ArticleVariantRecalibration, numBadVariants, and size of the data set
I'm somewhat struggling with the new negative training model in 2.7. Specifically, this paragraph in the FAQ causes me trouble: Finally, please be advised that while the default recommendation for...
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(BP2.0) Variant Discovery
This article is part of the Best Practices workflow document. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow. Once you've pre-processed your data according to our...
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(BP2.3) Variant Quality Score Recalibration
This article is part of the Best Practices workflow documentation. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow. The GATK callers (HaplotypeCaller and...
View ArticleInterpreting VQSLOD and Tranche Quality in a Non-Human Model Organism
Hello there! Thanks as always for the lovely tools, I continue to live in them. Been wondering how best to interpret my VQSLOD plots/tranches and subsequent VQSLOD scores. Attached are those plots, and...
View Articlehow to run VQSR for individually called samples for rare variant discovery
We are running GATK HaplotypeCaller on ~50 whole exome samples. We are interested in rare variants - so we ran GATK in single sample mode instead of multi sample as you recommend, however we would like...
View ArticleError Stack trace after running SelectVariants
I just wanted to select variants from a VCF with 42 samples. After 3 hours I got the following Error. How to fix this? please advise. Thanks I had the same problem when I used "VQSR". How can I fix...
View ArticleVQSR and Snpcall strategies for readgroups with different coverage distributions
Hi - I have a question on how best to do VQSR on my samples. One of the readgroups for my individuals are from genomic DNA and have very even coverage (around 10x) while the remaining 4-5 readgroups in...
View ArticleVQSR and Snpcall strategies for readgroups with different coverage distributions
Hi - I have a question on how best to do VQSR on my samples. One of the readgroups for my individuals are from genomic DNA and have very even coverage (around 10x) while the remaining 4-5 readgroups in...
View Articlebest 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...
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