How does HaplotypeCaller discriminate between heterozygous and homozygous...
Dear members of the GATK team I am using different GATK modules to detect some SNPs in my RNASeq data set. I did a test run for one individual to get an idea about the output of HaplotypeCaller. I know...
View ArticleAF calculation in Mutect2
Hi, I've been calling somatic mutations with Mutect2, and have noted that the AF calculation does not always correlate to DP alt/(DP ref+DP alt). For example, consider this indel: T057.mutect2.vcf:7...
View ArticleHaplotype Caller Makes SNPs look like INDELS
I'm using the HaplotypeCaller to look at SNPs related to antimicrobial resistance and am getting a result that looks like this: NC_011035.1 2049708 . CCGGCG C ... NC_011035.1 2049714 . C CAAGAA ... I...
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 ArticleWhen I call Indels from my vcf file using GATK analysis tools I ger an Error!
Hi I used the GATK pipeline until I got a vcf that had SNPs and Indels, so I used GATK Analysis tools to remove SNPs and keep Indels. But after adding the reference genome, dictionary and index I get...
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 ArticleProblem with LiftoverVcf
It is my first time running the LiftoverVcf, but I saw that many other users passed through difficulties similar to mine but not exactly the same. I'm trying to convert a vcf file from Hg18 to Hh19....
View ArticleThe result of Mutect BAM and vcf is different.
I got some vcf result using mutect. but I have some question about the result. the Allele frequency in vcf is so strange. for example, the below is my result. chr4 1809127 . C T ....
View ArticlePicard LiftoverVcf
I am having a problem with picard's LiftoverVcf. I am trying to Liftover hapmap files (downloaded plink files from hapmap and converted to vcf using plink) from ncbi36 to hg38. I was able to do this...
View ArticleHaplotype caller BP_RESOLUTION :More AD values than alleles called for
My intention is to find different bases called in a particular chromosome location irrespective of it being assigned as SNP/badbase. I user the below command: java -jar 3.5/GenomeAnalysisTK.jar -T...
View ArticleUse vcf from HaplotypeCaller as normal_panel with Mutect2 (GAKT4.beta.6) ?
Hi, I am trying to find somatic mutations in blood samples. The same samples were used previously to detect germline variants with HaplotypeCaller. Does it make sense to use the vcf obtained for a...
View ArticleError in SortVcf
I have been going through this problem. Is this very common and is there any solution to this error. Exception in thread "main" java.lang.IllegalStateException: Key . found in VariantContext field INFO...
View ArticleMinor Allele Frequency filter in GATK
Hi all, I'm working on a resequencing dataset , which contains 60 individuals from 5 different populations. I used HaplotypeCaller to conduct variants calling, and got all individuals in one big...
View ArticleErrors about input files having missing or incompatible contigs
These errors occur when the names or sizes of contigs don't match between input files. This is a classic problem that typically happens when you get some files from collaborators, you try to use them...
View ArticleWhat input files does the GATK accept / require?
Analyses done with the GATK typically involve several (though not necessarily all) of the following inputs: Reference genome sequence in FASTA format Unmapped sequencing data in uBAM format...
View ArticleErrors about input files having missing or incompatible contigs
This doc has been replaced by https://software.broadinstitute.org/gatk/documentation/article?id=11012 These errors occur when the names or sizes of contigs don't match between input files. This is a...
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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 ArticleGenotypeGVCFs: Long runtime exclusively with a single sample
I have been having some trouble with long runtime with several of GATK utilities. However it was manageable. I could arrive at a g.vcf file( I used HaplotypeCaller instead of UnifiedGenotyper upon a...
View ArticleHow to now if a Combined vcf file is calibrated with GATK or not
Dear GATK using community Pardon me for my ignorance, but I am new with using NGS pipelines. I have recieved a combined VCF file or 200 samples. The only information I was able to understand from VCF...
View ArticleSelectVariants error
I`m calling SNP by haplotype caller,and i got vcf document for each sample. After that , i use selectvariant to select variants of SNP . But i got this error: ##### ERROR...
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