DepthOfCoverage fails with java.lang.ArithmeticException: / by zero
I get the following error while executing DepthOfCoverage: Arguments: -T DepthOfCoverage -R /seq/regev_genome_portal/RESOURCES/human/Hg19/Hg19.fa -I...
View ArticleGATK4 BaseRecalibratorSpark , Executor heartbeat timed out after X ms
Hello, i'm trying to run GATK4 BaseRecalibratorSpark in local in a nextflow pipeline, but I got every time the same error with this command : gatk-launch BaseRecalibratorSpark --spark-runner LOCAL...
View ArticleCigar after picard MergeBamAlignment
Hi, I got confused by the CIGAR in bam file. after MergeBamAlignment. I have reads in uBam. Then it's converted into fastq and trimmed on 5' side. Then aligned with STAR and MergeBamAlignment the...
View ArticleGATK4beta6 annotation incompatibility between HaplotypeCaller and...
Happy New Year! I'm attempting to joint genotype ~1000 exomes using GATK4. I've run HC per sample with the following command: java -Xmx7g -jar gatk-package-4.beta.6-local.jar HaplotypeCaller -ERC GVCF...
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(How to) Mark duplicates with MarkDuplicates or MarkDuplicatesWithMateCigar
This tutorial updates Tutorial#2799. Here we discuss two tools, MarkDuplicates and MarkDuplicatesWithMateCigar, that flag duplicates. We provide example data and example commands for you to follow...
View ArticleBAM header using BWA-MEM in galaxy compared with GATK resource bundle (hg38)
Hi! I am trying to perform CollectSequencingArtifactMetrics but I'm getting an error of the dictionary sizes. Long story short, I performed BWA-MEM using hg38 in Galaxy Project (https://usegalaxy.org)...
View ArticleReducing GATK/Picard tools Docker image size
Hi Team, I'm optimizing calls in a WDL (run on Google cloud), and while looking through the logs I realized that it takes full 3 minutes to pull broadinstitute/gatk image, which is now 3GB in size. I'm...
View ArticlePicard in Docker
Dear GATK/Picard team, I am new to Picard and was just about to build it, when I noticed that there is a Picard Docker image available - great idea! Is this functional yet? I couldn't find any...
View ArticleEverything looks "fine" when running RNA-SeQC, but RPKMs of all genes are...
Could anyone help me? I used STAR to do mapping and got the orded BAM file, and have added RG tag, Markdupicate and Index by picard successfully. But encounter problem when running...
View ArticleCan GenotypeGVCFs be ran without filtering?
For bacteria genomes I use the "Best Practices" and the HaplotypeCaller to call variants. I would like to output a VCF containing all positions I can then parse on my own. I'm using -ERC BP_RESOLUTION...
View ArticleHaplotypeCaller in Gatk4 vs Gatk3.5
Dear colleagues, I noticed that latest "5 dollar pipeline" uses HaplotypeCaller from gatk3.5 not gatk4. Could you comment is it OK now to use HaplotypeCaller from gatk4 - if no, what are potential...
View ArticleBwa command line parameters at 5 dollars pipeline
Dear colleagues, I see bwa_commandline="bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta" at 5 dollars pipeline but bwa does wrong things this way. When I use "-p" parameter it does produce only...
View ArticleGATK4 - VariantFiltration --genotype-filter-expression
Hello there, I am trying to apply some sample-level filters on a VCF generated using GATK4.0.2.1. My issue is that all variant sites are not getting an FT flag added and I am wondering why....
View ArticlePut the reference files on hdfs or in local directory when using spark tools...
Hi, does anyone know whether we should put the reference files on hdfs or in some local directory on each datanode? I did not find any examples about this. Could anyone help? Thank you!
View ArticleLoosing variants when indel realignment step is omitted
I have inherited a number of 2x sequences which were processed in large with agreement with the Best Practices. One thing which could be improved upon in the pipeline was deleting the redundant step of...
View ArticleCan I use arbitrary genomic intervals in GemomicDBImport
Hello, I'm facing a problem of making variant calls from ~1500 WGS samples. I have successfully run HaplotypeCaller by breaking the "wgs_calling_regions.hg38.interval_list" which comes with the GATK...
View ArticleGATK 4 support on AWS
Hi, Just wanted to check on the status of support for GATK 4 on AWS. The most recent I read was that there was support only for google cloud. We are working with a vendor to run GATK 4 and their tool...
View ArticlePanel of Normals (PON)
A Panel of Normal or PON is a type of resource used in somatic variant analysis. Depending on the type of variant you're looking for, the PON will be generated differently. What all PONs have in common...
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FastQC showed me my raw data has 2 peaks in the GC content tab
Hello, I just got my FFPE samples back from the sequence provider, I see a double peak like in the image, what does it mean? Should I be worried? Is this normal for FFPE samples? It was a single pair...
View ArticleHaplotypeCaller (gvcf mode) on whole genome vs chromosome by chromosome
I'm currently running my first real use of GATK. I was worried about running HaplotypeCaller on whole geneomes given some of the reports I've seen on these forums about how long it can take to run. In...
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