Picard MarkDuplicates Barcode Tag
Hello! I was wondering how the implementation of MarkDuplicates differs when the --barcode_tag option is specified and I haven't been able to find anything in my searches. I'm terribly sorry if this...
View ArticleDoes trimming affect the variant calling?
Dear GATK team, I am aware that you do not particularly recommend adapter or quality trimming, as discussed here:https://gatkforums.broadinstitute.org/gatk/discussion/2957/read-trimming However, does...
View ArticleWhy GenomicsDBImport is not taking the argument...
Dear GATK team, The following error message I am getting, when I am trying to update my existing datastores with some new g.vcf files:-...
View ArticleBadly formed genome unclippedLoc: Query interval "20" is not valid for this...
Hay, I tried using GenomicsDBImport with 28 samples. I tried to load my data using a sample map file (tab separated sample header and their absolute paths) but on using the command - gatk...
View ArticleSelectVariants halted without an error
This discussion was created from comments split from: GATK v4.1.3.0: Error with SelectVariants.
View ArticleGermline copy number variant discovery (CNVs)
Purpose Identify germline copy number variants. Diagram is not available Reference implementation is not available This workflow is in development; detailed documentation will be made available when...
View ArticleIf the HaplotypeCaller support FPGA Acceleration Cards of Xilinx?
we want to implement HaplotypeCaller Acceleration by Xilinx FPGA Acceleration Card, I know that support by Intel FPGA A10 Cards, if support by Xilinx FPGA card also? THX :)
View Articlegatk FilterVariantTranches
I am a bit unsure on the usage of FilterVariantTranches. I have have applied CNNScoreVariants to a VCF and am now trying to filter. I am using another VCF as the resource (also after applying...
View Article0 variants lifted over but had mismatching reference alleles after lift over
Hi, guys: I am trying to liftOver a VCF file. Please see my log file below. There does not seem to have an error, but somehow none of my SNPs are lifted over. Can someone please let me know what is...
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RNAseq short variant discovery (SNPs + Indels)
Purpose Identify short variants (SNPs and Indels) in RNAseq data. Reference Implementations Pipeline Summary Notes Github Terra RNAseq short variant per-sample calling BAM to VCF universal (expected)...
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GATK4 CNV, output 3 million CNVs !!!
Hi, there: I was very excited to know that GATK4 could now generate CNV data from WGS. However, I spent long time to make it work, but I think it still does not. I recently followed all the...
View ArticleMarkDuplicatesSpark not respecting --conf 'spark.executor.cores=4' option
Hi, I'm trying to run gatk MarkDuplicatesSpark (v 4.1.4.1) locally, so not on a spark cluster, and provided the option --conf 'spark.executor.cores=4' to tell MarkDuplicatesSpark to use only 4 cores on...
View ArticlegermlineCNVCaller Procedure
Hello, I am trying to use the gCNV caller to call CNVs in a large set of samples. I am trying to figure out how to do so, but am quite confused as to the proper steps to take, and inputs and outputs...
View ArticleGATK 4.1.4 DenoiseReadCounts: Sample intervals must be identical to the...
Hi I've been getting failures in Terra from the most recent 2-CNV_Somatic_Pair workflow copied from help-gatk/Somatic-CNVs-GATK4 that has an error message: 18:58:30.763 INFO SVDDenoisingUtils -...
View Articleappropriate members for generating "known-sites" list
I have 46 complete genomes and a good reference genome. Two of the individuals are "outgroups" (two different species). The rest are the same species as the reference genome. One of the outgroups...
View ArticleSafe to use HaplotypeCallerSpark?
Hi all, I'm wondering how bad it is to use use HaplotypeCallerSpark in GATK 4.0.2.1/JDK 1.8? I realize it's in beta, but I'm wondering if that means "your results will be useless" or just "use with...
View Articlewhat is the current page for VCF hard-filtering?
Hi GATK people, I am preparing a training session using 4.1.4.1 and would need the current official list of parameters for hard filtering of hg38 VCF data. I also demonstrate the VQSR but for...
View Article(How to) Filter variants either with VQSR or by hard-filtering
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section. This article outlines two...
View ArticleHaplotypeCaller successfully generated my g.vcf.gz, no error message but exit...
Hi the gatk team, I used HaplotypeCaller to generate a vcf file. Everything went fine : I got no error message, the vcf.gz and the vcf.gz.tbi were generated , however, the exit status was not '0' but...
View ArticleError of INDEL mode during VQSR process
Hello, I'm trying to do VQSR on exome data of 50,000 samples. Since this dataset is too big, I used GenomicsDBImport to merge. Whole exome merging is also slower than expected, so I did this per...
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