VCF file and allele frequency
Hello All, I am using I am using GATK RNA-seq variant pipeline for finding muttaion/vatiants on the list of gene given in teh follwoing command line java-1.7 -jar -Xincgc -Xmx1586M...
View ArticleVCF validation...
Dear All, We have a pile of full-genome sequences from fish genomes, and we're trying to call variants so that we can look for P-G associations. Given the genetic distance between some of our samples,...
View Articleexample vcf file from mutect2
Would it be possible to get an example vcf file from the mutect2 tool, to use to testing tools for displaying the variants? The files I have have private data that can't be shared.
View ArticleLarge number of scaffolds for the reference genome for SNP calling pipeline
Hello, I am running the SNP calling pipeline from RNA-seq data. I used STAR for alignment. My reference genome is composed of 32012 scaffolds from which more than 30000 are contigs with length of less...
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 ArticleSNP calling on inverted repeats
Dear GATK team, I have encountered a problem when I used the HaploTypeCaller for variant detection on about 100 plastid genomes. The plastid genome is haploid and contains two large inverted repeats...
View ArticleAn error happened in CombineGVCFs :Unable to create iterator for rod named...
Hello everyone, I met an error when I do combineGVCFs with the command line as follow: java -Xmx500g -Djava.io.tmpdir=goat_pan/tmp -jar GenomeAnalysisTK.jar -R ASM.fa \ -T CombineGVCFs \ --variant...
View ArticleHow to explain a variant present in PON is classified as PASS in the output...
How to explain a variant present in PON is classified as PASS in the output (do not filtered as panel_of_nomal) using Mutect2. The VCF corresponding to this variant in the PON file (called normal.vcf)...
View Articlemutect2 output filter field
Hi! I ran mutect2 and I got the vcf file, but I didn't understand the output. For example I have this line in my vcf: CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample13 chr1 10715958 . T...
View Articleg.vcf masks variants with conflicted reads
I'm working on Salmonella, and one of the major sources of noise in our analysis is that there are some regions of the genome where we have many reads that disagree with the eventual call at that...
View ArticleASEReadCounter contruct a heterozygous VCF input file for all nucleotides in...
The aim is to identify any and all bi-allelic SNPs in my region of interest. Then determine if there is allelic imbalance in all my RNA-seq samples. I already filtered the BAM files for the region of...
View ArticlecombineGVCF batch effects
Dear Sir/Madam, We have been using the best practice variant calling pipeline to call variants in our targeted sequencing data (GATK 3.2.2). Me and others in the team have discovered batch effects in...
View ArticleFastQ to VCF - known indels and SNPs VCF files as vcf.gz
Hi, I have followed the GATK Best Practices to go from fastQ to VCF files with success thanks to the great documentation you have! I would like to know if the known indels and SNPs VCF files passed to...
View ArticleProblems of common variants substraction after using CombineVariants
Hello everybody, I am currently working on WGS data from C. elegans genome resequencing. I am trying to improve the substraction of common variants shared by multiple mutant strains. After in silico...
View ArticleVariantEval "stuck" on 1 position
Hi there As in title, i am observing that VariantEval would get stuck in a given position for a very very long time (so long my job on a cluster would get cancelled). I've checked and it is not an...
View Articleburden test/SKAT on exome study without control
hi, We have access to exome-sequencing data from an independent set of leukemic samples from a mouse model with an induced oncogene. However, these samples do not have an associated paired (normal)...
View ArticleMESSAGE: Code exception (see stack trace for error itself)
Hi all, I meet some error while call variant with HaplotypeCaller, please help~~ Thanks a lot! my CMD: java -Xmx20g -jar GenomeAnalysisTK-3.6.jar -T HaplotypeCaller -R /human_g1k_v37_decoy.fasta -I...
View ArticleError in FastaAlternateReferenceMaker
Dear GATK Team Greetings I am facing error with FastaAlternateReferenceMaker in order to generate an alternate reference fasta file which include of indels form VCF file. I executed command as follows...
View ArticlePhaseByTransmission reassigns genotype code that conflicts with the allelic...
I encountered a problem running PhaseByTransmission (PBT) module on female proband with both healthy parents. Prior to running the module, the correct genotype was assigned to the Father but after...
View ArticlePiping for Picard and GATK
Could someone please tell me which tools in Picard and GATK can use pipe? Right now, I am using Picard: SortSam, MarkDuplicatesWithMateCigar, AddOrReplaceReadGroups GATK: RealignerTargetCreator,...
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