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HS_LIBRARY_SIZE = "" (that's right, nothing, empty) HS_PENALTY_XX are all 0
So I've ran both the newest version of Picard CollectHsMetrics and an older version CalculateHsMetrics and with both versions I'm getting statistics for everything but the HS_LIBRARY_SIZE which has an...
View ArticlePicard SortVcf changing VCF file version
I am using Picard SortVcf to reorder the order to match the order of my reference genome and BAM files. And it works great, however it seems to be changing the VCF format from 4.0 to 4.2, and this is...
View Articleinstalll GATK 4.beta.5
1.download gatk-4.beta.5.tar.gz 2. tar zxvf gatk-4.beta.5.tar.gz 3. cd gatk-4.beta.5 4. ./gradlew bundle bug: FAILURE: Build failed with an exception. * Where: Build file...
View ArticleTest sample data of GATK Best Practice
Hi GATK team, I want to know test-data set of GATK Best Practice. My aim is check GATK4 perfect-run on my environment. Especially, from "fastq and reference" to variant-called-vcf file. (both Germline...
View ArticleShould I remove unmapped bam files from the data for variant calling analysis?
I heard GATK uses unmapped bam during realignment. So is it necessary to remove unmapped regions in bam file?
View ArticleRe-starting GenotypeGVCFs from certain position?
Hi, I was joint genotyping about 400 samples with GenotypeGVCFs when I had node failure. The run was at about 83% which two weeks to get there. Is there a way for me to continue from this position...
View ArticleMutect2 --artifact_detection_mode
I have a question how to create Panel of Normals (PON) using Mutect2: do we still need to add the dbSNP and Cosmic parameters when running the following command for each normal BAM in...
View ArticleERROR MESSAGE: Unable to read index file, for input source:
Hi,GATK term I have set up a bwa + gatk best pratices pipeline for variant calling on pannel data(700 samples ). I use the haplotype caller in gvcf mode.The bam to the gvcf commands is : java -Xmx20g...
View ArticleI need help. GATK Haplotypecaller says my dict is empty but it isn't??
The Error message I get is the following INFO 12:25:14,659 HelpFormatter - ---------------------------------------------------------------------------------- INFO 12:25:14,662 HelpFormatter - The...
View ArticleGATK 3.8-0 PrintReads fatal error
Hello, Could you please help me to figure out this fatal error in running PrintReads? After I updated GATK to version 3.8-0. I kept getting this fatal error in running PrintReads. I can skip this step...
View ArticleHow do I submit a detailed bug report?
Note: only do this if you have been explicitly asked to do so. Scenario: You posted a question about a problem you had with GATK tools, we answered that we think it's a bug, and we asked you to submit...
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GATK4 run on spark cluster,-Unable to find _SUCCESS file
Hello： I tried GATK4 on spark cluster ,but the output bam result could not on my spark output path (HDFS). A USER ERROR has occurred: Couldn't write file /user/zhusitao/output/Mbam because writing...
View ArticleIs there any way to generate interval list from available exome data?
Hi all, I am following the "best practice" suggested by broad institute to call variants from whole exome sequencing data. Currently, I am using Mutect2 to call variants from tumor sample and normal...
View ArticleChange format of AD field to Number=R?
Hi In GATK version 3.5 I see the following in VCF headers: ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> However, the number...
View Article(howto) Recalibrate base quality scores = run BQSR
Objective Recalibrate base quality scores in order to correct sequencing errors and other experimental artifacts. Prerequisites TBD Steps Analyze patterns of covariation in the sequence dataset Do a...
View ArticleTutorial data not accessible anymore?
Hi, I am trying to follow the tutorial (https://software.broadinstitute.org/gatk/documentation/topic?name=tutorials) but unfortunately the data are not accessible anymore. I tried to get some via...
View ArticlePicard IlluminaBaseCallsToSam - clocs file issue - more elements than expected
I am attempting to demultiplex a lane of Illumina HiSeq2500 data using Picard IlluminaBasecallsToSam (v2.5, Java(TM) SE Runtime Environment (build 1.8.0_20-b26)). This tool fails to complete and states...
View ArticleShould CheckIlluminaDirectory be able to handle a non-standard read structure
I have a flowcell (from a 10x library) in which the 'natural' read structure is 178T8B14B5T. However, I want to interpret the flowcell as 178T8B14T5S, so that is what I passed to...
View ArticleTutorial files provenance: ASHG15
This document is intended to be a record of how the tutorial files were prepared for the AHSG 2015 hands-on workshop. Reference genome This produces a 64 Mb file (uncompressed) which is small enough...
View ArticleNot enough memory for depth of Coverage as single thread
Hi, if I run depthOfCoverage without -nt it crashes somewhere in Chromosome 11 with ERROR MESSAGE: An error occurred because you did not provide enough memory to run this program. You can use the -Xmx...
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