(howto) Test your GATK installation
Objective Test that the GATK is correctly installed, and that the supporting tools like Java are in your path. Prerequisites Basic familiarity with the command-line environment Understand what is a...
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Picard haplotype map file format
The haplotype map that certain Picard tools require is a file that maps SNPs to LD (linkage disequilibrium) blocks. These tools include Picard CrosscheckReadGroupFingerprints and CheckFingerprint. For...
View ArticleAdvice on troubleshooting 'ERROR MESSAGE: Badly formed genome loc'
Hi I am getting the following error message using IndelRealigner in GATK 2.8.1 ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 114033418 is less...
View Articlepicard CrosscheckReadGroupFingerprints
Hello, In the picard CrosscheckReadGroupFingerprints command, it asks for a Haplotype_map file. What format does Haplotype_map file need to be in? If you have multiple BAM files with the same RG tag,...
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Errors about contigs in BAM or VCF files not being properly ordered or sorted
This is not as common as the "wrong reference build" problem, but it still pops up every now and then: a collaborator gives you a BAM or VCF file that's derived from the correct reference, but for...
View ArticleDownload Oncotator Datasources
Hi, I would like to run Oncotator locally but was unable to find the latest datasources on the broadinstitue ftp servers. Could somebody please point me to the latest files? Best regards, Christophe
View ArticleHaplotypeCaller error: A fatal error has been detected by the Java Runtime...
Hi, When I am using HaplotypeCaller on a recently updated system, I always got an error message like this: # A fatal error has been detected by the Java Runtime Environment: # SIGSEGV (0xb) at...
View ArticleRunning MuTect error Malformed walker argument: Could not find walker with name
Dear all hi, I am aware that this problem has been posted couple times, however I have not seen a working result for me thats why forgive my ignorance. I have a pair of tumor and normal bam files...
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Problems interpreting Mutect2 output
Hello, I am calling variants with Mutect2 (default parameters) from bulk WGS Tumor/Normal pairs following Somatic SNV Best Practices, and in the VCF outputs I am finding a lot of variants like this...
View Articlejava.lang.reflect.InvocationTargetException for Combine Variants
Hello, I have a number of multiple individual vcf, which are large in size (average ~ 40 gb) and I am trying to combine them into one vcf. However, when I try to CombineVariants, an error message is...
View ArticleNew interactive support feature in GATK4
You may have heard that we've been working on a major new release of GATK that we call GATK4. As we are getting closer to the scheduled transition of GATK4 into beta status (from its current lowly...
View ArticleWhy "NO_READS" from DiagnoseTargets despite lots of reads in interval?
I a m running DiagnoseTargets on a list of intervals corresponding to targeted exons. In the result file, intervals are filtered by i.e. PASS, LOW_COVERAGE, COVERAGE_GAPS or NO_READS for each sample as...
View ArticleFasta Alternate Reference Maker Ignoring Insertions
I seem to be having an issue with the Fasta Alternate Reference Maker. Within my bam file and well as the vcf file there are notated insertions in 100% of the reads. When a fasta is created this...
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(How to) Call somatic copy number variants using GATK4 CNV
Presented tools are in BETA. 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....
View ArticleIs it necessary to process 1000 genome data for exome variant calling training?
I have an independently sequenced human exomes with 100x coverage. I would like to call variants using the GATK best practices guidelines, and have been following the guide to do so. However, I am...
View Articlemissing mutation in TP53
Dear all, we have been doing a WES analysis, and we have used MUTECT2 to call the mutations in a situation where we had : 1) -- a tumor sample 3) - unpaired 3 germline samples (that 've pooled...
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HaplotypeCaller and detection of large indels
Hi, I am wondering about the detection of large indels with the haplotypecaller. I have an example where to my mind there is quite clearly a large deletion (a couple of kb) in the sample, but it is not...
View ArticleGATK didn't Output the InDel I expected
Hi! I used GATK to call InDel and SNP with my sequence data. But GATK didn't give any output variations(InDel and SNP). So, I use GATK to generate a "bamout file" showing how HaplotypeCaller has...
View ArticleGATK best pratices for RNA-seq somatic mutation finding
Dear All, I have followed GATK best practices for finding Somatic mutations from cancer versus normal sample from RNA-seq data using Mutect2 as the final caller and rest all quality control steps as...
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