GenotypeGVCFs: --includeNonVariantSites disappeared?
Hi, I just wanted to use the GenotypeGVCFS tool to genotype some gvcfs at known variant sites and am also quite interested if my samples are reference at these positions or if the sites are not...
View ArticleQuality trimming
Hi GATK team, I was wondering, your best practices for data preprocessing (https://software.broadinstitute.org/gatk/best-practices/workflow?id=11165) don't mention any trimming (using i.e. trim_galore...
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Germline short variant discovery (SNPs + Indels)
Purpose Identify germline short variants (SNPs and Indels) in one or more individuals to produce a joint callset in VCF format. Reference Implementations Pipeline Summary Notes Github FireCloud Prod*...
View ArticleGATK4.0.2.1: steps, interval list, precision of the range (interval)
Hi, I'm still a little confuse about intervals. For example, personally I use the -L option in the following steps (-L intervals, -R reference genome): BaseRecalibrator (-L): chr1... chrX, chrY (...
View Articleskip "indel realignment" and recalibration"
Hi to all can I skip "indel realignment" and re-calibration" steps, when I am using HaplotypeCaller ?
View ArticleSortSam before MarkDuplicates?
Hi GATK team, I'm setting up a GATK best practices workflow. It is described here: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11165 that after mapping, which I did like this:...
View ArticleCombineVariants-- inconsistent references error
Hi I have 2 vcf files vcf1 from WGS data vcf2 from genotype data I am trying to merge these two files using combinevariants java -jar $GenomeAnalysisTK_jar -T CombineVariants -R $REF --variant $vcf1...
View ArticleCan GATK 4 output all reference sites after joint genotyping?
Hi GATK, My question is if its possible to run --includeNonVariantSites in GATK 4? Ari
View ArticleHaplotypeCaller on whole genome or chromosome by chromosome: different results
Hi, I'm working on targeted resequencing data and I'm doing a multi-sample variant calling with the HaplotypeCaller. First, I tried to call the variants in all the targeted regions by doing the calling...
View ArticleMutect2 does not recognize reference sequence
Hi GATK team, I'm trying to run the Mutect2 pipeline on build 38 WGS CRAM files. I am using something very similar to this WDL:...
View ArticleInvalid command line: Cannot process the provided BAM/CRAM file(s)
I am trying to generate a joint call VCF file from two bam files. Here is my code : java -jar /usr/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R ucsc.hg19.fasta -I 1-A10_S10.bam -I 1-A11_S11.bam...
View Articleerror_java.lang.IllegalArgumentException: No data found--when using VQSR
ERROR ------------------------------------------------------------------------------------------ ERROR stack trace java.lang.IllegalArgumentException: No data found. at...
View ArticleWhen should I use -L to pass in a list of intervals?
The -L argument (short for --intervals) enables you to restrict your analysis to specific intervals instead of running over the whole genome. Using this argument can have important consequences for...
View ArticleCombineGVCFs error in GATK 4.0.1.2
Hi, I am aware that some people have faced this error, but they are from old version of GATK and I am not sure if it applies to the GATK version I am using or not (4.0.1.2 with Java 1.8.0_74)..but I am...
View ArticleError stack trace when I try running GenomeAnalysisTKLite.jar.
Hello, so I know this may sound odd, but I have to use an older version of GATK for my company. We are using 2.3.0 and when I try running it on a new machine I get. `##### ERROR...
View ArticleSeveral Annotations not working in GATK Haplotype Caller
I am using Genotype Given Allele with Haplotype Caller I am trying to explicitely request all annotations that the documentation says are compatible with the Haplotype caller (and that make sense for a...
View ArticleCan GATK mutect2 detect MNPs?
In GATK 3.8, we used readbackedphasing to merge SNPs into a MNP, but I did not see this tool listed for 4.0 Does mutect2 do this now? Thanks
View ArticleHow Can I merge haplotypes to MNPs in GATK4
I was using GATK 3.8 previously, and I identify MNPs in haploid sequences by first using HaplotypeCaller and GVCFs and then ReadBackedPhasing using the enableMergeToMNP option. But GATK4 seem to have...
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Does GATK HaplotypeCaller has resume analysis feature
Hello there, I am calling variants on 800 exome samples using Haplotypercaller for some reasons the caller stopped the analysis on certain location on chromosome 5 (after 5 weeks and i have 10 weeks to...
View ArticleVariantFiltration: how to filter samples where less then 95% of reads agree...
I've been looking over the documentation for VariantFilteration and jexl...
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