GVCF generated from lane-wise bam and merged bam
Dear GATK Team, I ran GATK4 variant calling as per best practices on one WGS sample sequenced in lanes. Steps followed to get MergedBAM : Aligned lane wise fastq separately, remove duplicates, merge...
View ArticleChanging GATK base quality score input
I am working with low quality data from a non-model organism. The average base quality in my reads is about 28. Are there any flags in GATK4 (or GATK3) that will lower the base quality threshold so...
View ArticleExecuting gradlew script gives IOException:Function not implemented
Hello there, I would appreciate some help since I was just trying to build the 4.0.5.1 version but I was unable to success. I checked my Java version which is: openjdk version "1.8.0_191" OpenJDK...
View ArticleHow do you generate the file required for the --contig-ploidy-priors parameter
I have been attempting to use the new germlineCNV caller tool and compare it the XHMM but am having a very difficult time running the DetermineGermlineContigPloidy function in cohort mode in gatk. My...
View Articleissues with FindCoveredIntervals
Hi, I'm using FindCoveredIntervals with GATK 3.8 and running the following: java -jar GenomeAnalysisTK.jar -T FindCoveredIntervals -R reference.fasta -I input.bam -cov 10 -minBQ 30 -minMQ 30...
View ArticleIssues in Filtering by AF
Hi, I have used the GATK pipeline and generated vcf files after using Haplotypecaller, GenomicsDBImport and GenotypeGVCFs. I am working with a non model organism and I am currently filtering the...
View ArticleGATK4 Mutect2 variants IDs not shown
Hi everyone! I am a beginner using GATK, so bear with me please. Also, I am sorry this is duplicated in Biostars, I believe here is more appropriate. I am trying to do my variant calling with GATK4 new...
View ArticleConstruct genome with gvcf or vcf file?
I have 100 rice accessions and their mapping files from DNA sequencing. My goal is to construct the genome for a specific region for each rice accession. Could I just use the gvcf file after initial...
View ArticleGenotype Concordance: Logic behind defined values
Hi there, I am currently using GenotypeConcordance through picard to generate a summary of the concordance between two different sets. One set, a plasma sample, is regarded as the truth, and the other,...
View Articlegvcf or final vcf used to construct accession specific genome
I have 100 rice accessions and its DNA sequencing bam files. My goal is to construct the genome in a specific region for each rice accession. Could I directly use the gvcf file from the variant call?...
View ArticleGATK resource bundle
This discussion was created from comments split from: New to the forum? Ask your questions here!.
View ArticleWeird VariantRecalibration result, should i add exome data from 1000G project...
Hi, attached below is the result of running VariantRecalibration on the chr1 of 56 individuals? Seems like there is no true positive discovered. gatk VariantRecalibrator -R $reference -V...
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Haplotypecaller calls variants at a deletion region
Hi, I'm having a confusing problem when using haplotypecaller. Basically, I'm using haplotypecaller calling variants among more than 400 M. tuberculosis samples, sequenced with Hiseq2500 platform. I...
View ArticleHow to pre-assign the multiple regions I want to process in each pipeline?
Dear Genome STRiP users, I intend to process part of the chromosome in each pipeline rather than processing the whole sequence. I know there is an -L flag in the SVPreprocess, but it is not listed in...
View ArticleRegarding Different genotypes for same sample using Unified Genotyper &...
Hello Team, I am doing multi sample cohort exome analysis for which i have called SNPs using both callers (UG & HC).For one of my important SNP, i am observing different genotypes in few samples...
View ArticleDifferent variant calling result depending on the interval length using Mutect2
Hello, we are working with Mutect2 to call somatic variants (snvs and indels) on targeted sequencing. We recently have noticed an issue related to an specific variant detection, so that we detect it if...
View ArticleSplitNCigarReads: Hard clipping of overhangs
Hi, Running SplitNCigarReads doesn't seem to hard-clip intronic overhangs despite using aggressive clipping parameters I ran gatk (version: 4.1.0.0) with the following command gatk SplitNCigarReads -R...
View ArticleSVPreprocess Error: java.lang.OutOfMemoryError
Dear Genome STRiP users, I can successfully complete SVPreprocess to 3418 samples. However, when I enlarge the sample size to 10686, it returned an error as below and it seems like that the even after...
View ArticleVariants found in GVCF but not in VCF
Suppose the main difference between GVCF and VCF is the non-variant record. Curiously, I found some variants were called in GVCF but not in VCF. This is the variant I found in GVCF but couldn't found...
View ArticleWhat is uBAM and why is it better than FASTQ for storing unmapped sequence data?
Most sequencing providers generate FASTQ files with the raw unmapped read sequences, so that is the most common form in which the data is input into the mapping step of the pre-processing pipeline....
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