Which is the best way to handle "Mate alignment does not match alignment...
After running ValidateSamFile program on my bam files, I received following error message. ERROR: Record 417172897, Read name J00137:36:H5TFGBBXX:6:1121:30675:9772, Mate alignment does not match...
View ArticleVariant Filter
Hello, I have generated a multi sample vcf file with haplotype caller followed by CombineGVFs -> VariantReCalibrator -> Apply Recalibration. Now I would like to filter my variants (only SNPs)...
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 ArticleCombineVariants resets AF to 0.5 and 1.0
Dear GATK Team, I have been using CombineVariants to merge SNPs.vcf and Indels.vcf of the same sample into a single vcf file. In the SNP.vcf and Indels.vcf files, I have changed the value for AF tag in...
View Articlebcl2fastq and small test data
I am preparing a Docker image for running bcl2fastq 2.19. I would like to create an integration test using this Docker container with some small BCL data. I've tried...
View ArticleShould I use sorted.bam or clean_dedup_recalibrated.bam for getting the...
Recently we performed exome sequencing using Nextera Illumina platform for three samples (Father, Mother and Son). This time we used the new kit for exome sequencing. I am trying to collect the...
View ArticleRef Allele in MUTECT2 vcf
Dear all, happy and fruitful spring time ! this question may have been asked before, and just wanted to know please : the REF allele that is reported by MUTECT2 is according to the reference sequence,...
View ArticleHC step 4: Assigning per-sample genotypes
This document describes the procedure used by HaplotypeCaller to assign genotypes to individual samples based on the allele likelihoods calculated in the previous step. For more context information on...
View ArticleCan i use Apache spark to submit job to GATK?
Hi, I just found apache spark is very useful tool for submiting job. How can i use this for submitting job to GATK? Regards
View ArticleDescription and examples of the steps in the CNV case and CNV PoN creation...
The CNV case and PoN workflows (description and examples) for earlier releases of GATK4. For a newer tutorial using GATK4's v1.0.0.0-alpha1.2.3 release (Version:0288cff-SNAPSHOT from September 2016),...
View Article(howto) Apply hard filters to a call set
Objective Apply hard filters to a variant callset that is too small for VQSR or for which truth/training sets are not available. Caveat This document is intended to illustrate how to compose and run...
View ArticleGoogle Genomics - problem with regions/zones settings
While trying to run the GATK example at https://cloud.google.com/genomics/v1alpha2/gatk I get the following error Unsupported key/value pair in WorkflowOptions: defaultRuntimeOptions ->...
View ArticleSelectVariants is not recognizing a sample by name
Hi, I'm having a strange error when using the SelectVariants tool; when I try to extract one sample from a multi sample vcf (which I'm sure includes the sample) I get the following error message:...
View ArticleGenotypeGVCFs on pooled data sets fail for ploidy > 10
Hi, I'm currently analysing a data set of six pools, 25 individuals in each (ploidy 50), of a non-model organism. I initially ran HaplotypeCaller with parameter -ERC GVCF and then attempted to do joint...
View ArticleHow should I pre-process data from multiplexed sequencing and multi-library...
Our Best Practices pre-processing documentation assumes a simple experimental design in which you have one set of input sequence files (forward/reverse or interleaved FASTQ, or unmapped uBAM) per...
View ArticleThe contig order in reads and reference is not the same
Hello GATK team, I was about to run SplitNCigarReads tool in GATK3.7. Unfortunately there is an error regarding the input files reads and reference having incompatible contigs. input: java -jar...
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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 ArticleVariantsToBinaryPed: Convert VCF to binary pedigree file
Hi, To Convert vcf file into .bed, .bim , .fam i used here the following command java -jar GenomeAnalysisTK.jar -T VariantsToBinaryPed -R chr20_NOPREFIX.fa -V chr20.vcf -m metadata.fam -bed chr20.bed...
View Article--excludeAnnotation MLEAC MLEAF
Hello, I want to exclude the IDs MLEAC and MLEAF in the INFO column of my VCF, but using --excludeAnnotation MLEAC doesn't work. IN this question...
View ArticleDifferent results of haplotypecaller using Base Quality Recalibration Score
Dear GATK team, I have analyzed samples sequenced with an Illumina custom amplicon sequencing kit. I aligned samples with BWA mem algorithm and then I applied haplotypecaller following the suggestions...
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