VQSR Annotations
I'm curious about the experience of the community at large with VQSR, and specifically with which sets of annotations people have found to work well. The GATK team's recommendations are valuable, but...
View ArticleVQSR INDEL output error
Hi, I am new to GATK, I have been trying to figure a strange error that I haven't been able to resolve for days. Process so far. 1. Run UnifiedGenotyper per chr using -L option on ~ 130 samples 2....
View ArticleDoes setting the -out_mode flag in UnifiedGenotyper differently has different...
Hello, Does VQSR behave differently when the -out_mode flag in UnifiedGenotyper is set to EMIT_VARIANTS_ONLY as compared to EMIT_ALL_CONFIDENT_SITES. I think by using EMIT_ALL_CONFIDENT_SITES we might...
View ArticleVQSR Training
When performing VQSR, the data set has its variants overlapped with the training set, may I know if all the overlapped variants are used in the training or is it down sampled?
View ArticleWeird multi-sample [119] exome VQSR tranche plot
Hello, I am trying to run GATK on a sample of 119 exomes. I followed the GATK guidelines to process the fastq files. I used the following parameters to call the UnifiedGenotyper and VQSR [for SNPs]:...
View Articlehow can vqsr applied on small data set?
We have data from target sequencing genes (only targeted two genes). We analyzed the data by GATK pipeline. Since the data set is too small, we tried hard filtration on both SNP and indels. At the same...
View ArticleQuestion about recalibration
Hello, I have a new sequenced genome with some samples for this specie, I would like to follow the best practices but I don't have a dbsnp or something similar, but could I use the variants from the...
View Articlets_filter_level vs. tranche settings
Hi, I'm having a little trouble understanding the relationship between the -ts_filter_level and -tranche settings for VQSR. If I'm not mistaken the defaults are 99 and [100,99.9,99.0,90] respectively....
View ArticleNaN LOD in VQSR
Hi all, I'm running VariantRecalibrator on a SNP set (47 exomes) and I get this error: ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR...
View Articlemulti sample VQSR on single sample vcf files
Hi We have 100 samples run through the GATK unified genotyper and then we merged all the VCF files to run the multi samples VQSR. (merged was done using VCFTOOLS). What attributes we should use in this...
View ArticleSignificant difference in VQSR or VariantAnnotation between v1.6 and v2.2-10
Hi, I observed a significant difference of the variant call sets from the same exomes between v1.6 and v2.2(-10). In fact, I observed a significant decrease in the overall novel TiTv in the latter call...
View Articlequestion about odd result for VQSR
Hi, Recently I run into some odd observation in VQSR. I have 17 samples from a same family and I used all of 17 samples to call SNPs and after VQSR, I got the trench file like this: Variant quality...
View ArticleVQSR for indels
Hello, I am running Variant Quality Score Recalibration on indels with the following command. java -Xmx8g -jar /raid/software/src/GenomeAnalysisTK-1.6-9-g47df7bb/GenomeAnalysisTK.jar \ -T...
View ArticleVQSR error: "The provided VCF file is malformed at... "
I am seeing this error on single human WGS sample - The provided VCF file is malformed at approximately line number "x": there are 557 genotypes while the header requires that 1525 genotypes be present...
View ArticleSensibility/sensitivity of VQSR processed VCF
Hi all, I've somewhere in this site that before VQSR the FP rate is expected to be around 10% (I guess for UnifiedGenotyper). Are there some updated statistics for VQRS? For HaplotypeCaller? For...
View ArticleVQSR for multi-sample VCF
Hi, I've been going through the VQSR documentation/guide and haven't been able to pin down an answer to how it behaves on multi-sample VCF (generated by multi-sample calling with UG). Should VQSR be...
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Variant Quality Score Recalibration (VQSR)
Slides that explain the VQSR methodology as well as the individual component variant annotations can be found here in the GSA Public Drop Box. Detailed information about command line options for...
View ArticleWhat VQSR training sets / arguments should I use for my specific project?
VariantRecalibrator For use with calls generated by the UnifiedGenotyper The variant quality score recalibrator builds an adaptive error model using known variant sites and then applies this model to...
View ArticleMouse VQSR
I was wondering if anyone has used VQSR for a mouse related genome project. I am working with mm10 dbsnp and DNA-seq short insert data for multiple homozygous mouse samples. I have obtained decent...
View ArticleDoes callset derived from HyplotyperCaller need run through VariantAnnotator...
Hi, I just run HyplotypeCaller on a dataset. For the same dataset, I have run through Unified genotyper and then directly subjected the raw vcf from UG to VQSR step without the help of VariantAnnotator...
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