AnalyzeCovariates fails with error message "RScript exited with 1"
When you run AnalyzeCovariates to analyze your BQSR outputs, you may encounter an error starting with this line: org.broadinstitute.sting.utils.R.RScriptExecutorException: RScript exited with 1. Run...
View ArticleHaplotyper memory issue
Hi. I am running Haplotyper with the below command. java -jar /usr/local/lib/GenomeAnalysisTK.jar -T HaplotypeCaller -R /media/data1/02_SNP_flanking_GC_content/am45new.fasta -nct 1 -I...
View ArticleMuTect2 downsampling (-dfrac) - numbers don't match?
Hi - I have a pilot normal-tumor paired samples that are sequenced to ~300X. We are now doing downsampling and see what's the minimum coverage we need to capture the SNPs/INDELs found in the original...
View ArticleApply GATK MuTect2 to SRA file
Hi I am running GATK MuTect2 to two SRA files, java -jar GenomeAnalysisTK.jar -T MuTect2 -R hg19.fa -I:tumor SRR537193.sra -I:normal SRR537200.sra -o SRR537193.output.vcf but received this error: ERROR...
View ArticleVariantRecalibrator: Values for MQRankSum annotation not detected for ANY...
Hi, I am running gatk, I met some problems, please help me find the solution thank you. when I run HaplotypeCaller, I used the code like the following: java -Xmx2g -jar $GATK -T HaplotypeCaller -R...
View Articlewhat is Compound Heterozygous ?
HI, http://gatkforums.broadinstitute.org/gatk/discussion/6455/biallelic-vs-multiallelic-sites after I read that ,I got a question : What is the difference between a biallelic mutation and compound...
View ArticleQD values
Hi I am working in the filtering steps, all my plots looks similar to your plots here, but the QD values are the opposite of what I am expecting, the most of the SNPs have values around 30. This means...
View ArticleWhich values are considered high coverage?
Hi all here you said that the SOR value is better than FS for filtering in high coverage data. When is considered high coverage? more than 20X? more than 30X? more than 50X? Best Wishes, Eric
View ArticleBiallelic vs Multiallelic sites
A biallelic site is a specific locus in a genome that contains two observed alleles, counting the reference as one, and therefore allowing for one variant allele. In practical terms, this is what you...
View ArticleException java.lang.NullPointerException when running multithreaded...
Running the multithreaded command below causes an error, although single threaded works fine. $ java -jar $GATK -T VariantFiltration -R human_g1k_v37.fasta -o chrom01_subset_biallelic_filtered.vcf...
View ArticleGATK4: ApplyBQSRSpark VS PrintReadsSpark
Hello there, What is the difference between GATK4 tools ApplyBQSRSpark and PrintReadsSpark? java -jar GenomeAnalysisTk-4_1.jar PrintReadsSpark -h suggests that output is String as shown below...
View ArticleMuTect2: complex variant expression
Hi, I use GATK3.7 MuTect2 to call somatic variant: here is the command: java -jar GenomeAnalysisTK.jar -T MuTect2 -R hg19.fasta -I:tumor tumor.bam -I:normal normal.bam --dbsnp dbsnp_138.hg19.vcf...
View ArticleNo plots produced by AnalyzeCovariates GATK4-Alpha
I'm using GATK4-Alpha AnalyzeCovariates java -Xmx80G -jar $GATK AnalyzeCovariates -before recal.table -after after_recal.table -plots recal_plots.pdf I then get the following error message referring to...
View ArticleVariant Recalibration failing
I'm trying to run variant recalibration for SNP as part of the GATK best practice workflow for DNA sequence analysis but am getting the following error presumably because after training there are 0...
View ArticleConflict between HaplotypeCaller variant and BAM
Hello, I'm using GATK version 3.6 to analyze a trio exome, and I followed the best practices (prinseq, bwa, markduplicates, baseRecal, printReads, HC and hard filtering, to resume the pipeline; with...
View ArticleWhy does my read-backed phasing skip a chromosome?
Hello, I am using GATK version 3.7-0 and i am performing read-backed phasing on WES data. While running the tool I noticed it skips the variants from chr7 for some reason. I checked the VCF and there...
View ArticleError: Unable to retrieve result, with "VariantRecalibrator"
My command lines are as following: java -Xmx8g -jar $CLASSPATH/GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R $GenomeReference \ -input $InputVCF \ -nt 6 \...
View ArticleHaplotypeCaller de-novo alignment discards reads
I am calling variants (SNPs and Indels) on WGS data. After JointGenotyping with g.vcf files I noticed that for some of the variants in the VCF file have a missing variant call (./.) despite having...
View Article--badLodCutoff option in VQSR
VQSR documentation says: "You may notice that these recommendations no longer include the --numBadVariants argument. That is because we have removed this argument from the tool, as the...
View ArticleRemoving annotations/genotype filters from a VCF?
Hello, We're preparing VCFs for public release. Our working VCF has a considerable amount of both info and format field annotations and also filters in both. We also have another header lines, such as...
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