Batch effects begone: Introducing the Functional Equivalence data processing...
By Eric Banks, Director in the Broad's Data Sciences Platform and original member of the GATK development team Ever since the GATK started getting noticed by the research community (mainly as a result...
View ArticleUsing GenomicsDBImport to consolidate GVCFs for input to GenotypeGVCFs in GATK4
In GATK4, the GenotypeGVCFs tool can only take a single input, so if you have GVCFs from multiple samples (which is usually the case) you will need to combine them before feeding them to GenotypeGVCFs....
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HaplotypeCaller reference bias in a nematode hybrid zone
I am analysing genetic variation across a hybrid zone between two strains of a parasitic nematode and find that my results are affected by the reference bias that GATK shows in low coverage regions. In...
View ArticleGRCh37/hg19: should I re-process my BAMs?
I have a human exome experiment on which I am using hg19 resources (reference, targets, dbSNP, ... the whole shebang). I want to add some 1000Genomes exomes to this experiment, but the available BAMs...
View ArticlePicard/GATK MergeVcfs throws errors
Dear all, I am following your guidelines for germline SNP detection in GATK 4. Nevertheless, I cannot complete the concatenation of region-wise gvcfs. Using GATK MergeVcfs I get the following error:...
View ArticleMutect2 Oncotator failed to delocalize files
I tried to run Mutect2 with Oncotator in FireCloud and it seems like Cromwell is having trouble copying files, though I don't know what that means. I got the following error message. Task...
View ArticleHuman b37 Indels/dbsnp annotation versions for IndelRealigner & BaseRecalibrator
Dear GATK Team, I have recently downloaded the GATK Bundle to get the human reference genome and its associated annotations. After the mapping step on my lane BAM files, I am planning on using...
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Calling variants in RNAseq
Overview This document describes the details of the GATK Best Practices workflow for SNP and indel calling on RNAseq data. Please note that any command lines are only given as example of how the tools...
View ArticleApplyBQSR - first and second pass re-calibration tables
I am following this run BQSR documentation which suggested generating first and second pass recalibration tables and analyze through AnalyzeCovariates . In GATK4, ApplyBQSR replaces this functionality...
View ArticleHow to properly merge bamouts after Mutect2
Hi, I ran Mutect2 (gatk4) using the -L command to split by chromosome, and the -bamout option. I am now using CatVariants (gatk3) to merge all the vcf files (one per chr) into a final vcf. And I also...
View ArticleUnable to determine status of job ID error
Hi, I occasionally get the following type of error when using genome strip CNVDisvovery pipeline on a cluster running SGE, it will run successfully for long periods of time and then arrive at this type...
View ArticleTesting Intel Arria® 10 GX FPGA implementation of HaplotypeCaller (PairHMM)
Hi, I am a researcher from Chinese of Academy of Sciences. I am trying to test the FPGA implementation of the HaplotypeCaller (PairHMM) on GATK 3.8-0-ge9d806836, using a Intel Arria® 10 GX FPGA (Arria...
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How can I identify the library ID in the fastq file name?
Dear NGS experts, I just started to analyse NGS data. I recently received some files that were generated at EMBL. I want to start analyzing them but have a hard time to figure out the read groups in...
View Articlefiltration of mutect2 results from GATK4
Dear staff, I just tried two ways of filtering the vcf file from Mutect2. First, I used variantfiltration which gives me 7 somatic sites. Actually I got 95 somatic variants in my vcf file. Then I tried...
View ArticleMINIMUM_GENOME_FRACTION - doesn't impact results on picard.jar...
I ran picard CollectGCBiasMetrics on 3 different bamfiles using 10 different settings creating a total of 30 plots. I found no difference between any of the results. MINIMUM_GENOME_FRACTION was set...
View ArticleHow can I use parallelism to make GATK tools run faster?
This document provides technical details and recommendations on how the parallelism options offered by the GATK can be used to yield optimal performance results. Overview As explained in the primer on...
View ArticleA GATK RUNTIME ERROR has occurred (version 3.1-0-g72492bb):
ERROR ------------------------------------------------------------------------------------------ ERROR stack trace java.lang.ExceptionInInitializerError at...
View Articlehow to solve the service registration corrupt error in your system.
if you face this type of error so you do not need to worry because we provide the solution of many problems just like service registration corrupt so you can visit my site and find the solution of your...
View ArticleIs it possible NAS stuck by CombineGVCF?
Dear GATK team, Recently, I used 4 CombineGVCF parallelly to combine 200 GVCF files for each chromosome on a NAS which is in raid 6 and the NAS has enough space to store the outputs. But the NAS got...
View ArticlePicard CollectRnaSeqMetrics chart reversed?
The gene coverage chart created by Picard CollectRnaSeqMetrics seems to be revered - the TES and the TSS are swapped. Typically poly-A selected libraries exhibit 3' (TES) bias, but the generated chart...
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