selecting/intersecting variants
Hello GATK, I have a WGS experiment of 3 genotypes from my favorite non-model organism for which I called variants based on GATK best practices (a pain for non-models!). I am interested in finding...
View ArticleWhat is the best practice for calling/combining variants across multiple...
Hi, I am working with RNA-Seq data from 6 different samples. Part of my research is to identify novel polymorphisms. I have generated a filtered vcf file for each sample. I would like to now combine...
View ArticleAllele frequency and depth VCF produced by MuTect2
Hi all, From my understanding of the VCF output, the AF[format] field (Allele fraction of the event in the tumor) equals to : AD[format] / DP[format]. With AD being the depth of coverage of each allele...
View ArticleMuTect2 is calling different variants when changing -minPruning value
Context : Working with targeted sequencing data (amplicon gene panel), depth is high, thus trying to adjust -minPruning value seems relevant. -minPruning argument : Paths with fewer supporting kmers...
View Articlewhich DP value shuold I use ？
I used HaplotypeCaller module to detect mutations,I noticed that the DP values was different in the INFO column and in the FORMAT column ,like the picture: Why this happened ?which DP value shuold I...
View ArticleMultisample vs Single sample(Paired sample MUT &WT separate BAM files)
Hello, I'm currently working with zebrafish mutants, and compare phenotypically wild-type and mutant siblings for mutations. I have 3 different mutants, like 3 pairs of different Mutant and Wild type...
View ArticleError in VariantAnnotator
hi Because my reference is in scaffold level and GATK not designed to analyse such referenes, thus my variant caller project done using samtools. Now i want to add QD(qualityofdepth) to vcf files using...
View ArticleFilteration creteria
i want to filter a vcf file resulted GATK. my criterias are QUAL < 30, FS > 60, MQ < 30, DP < 10 and GQ < 30. filterExpression in my command line in GATK must be as following? GQ is in...
View ArticleASECounter vs AD and DP in vcf file
Dear GATK developer: Can you please explain the difference between the allele counts obtained by running ASECounter and the allele read counts provided in the AD/DP fields in vcf file. It seems that...
View ArticleBamout file shows a consistent deletion that is not reported in VCF
Dear GATK team I ran HaplotypeCaller on a bam file, which is the alignment of a single bacteria sample to its reference genome. To understand the calling process I wanted to compare the resulting VCF...
View ArticleMutect2 output with samples with different read groups
Hi all, I am running Mutect2 with a tumour/normal match in RNA-Seq. Here is my command: gatk -T MuTect2 -R ./genome.fa --read_filter Mappin gQuality --min_mapping_quality_score 20...
View ArticleSome questions about VQSR.
Can I ask three questions about VQSR: 1. I have two VCF files from two different sources, and each of them contains several samples. The sequencing processes are basically the same (library prep,...
View Articlefastest way of getting total number of variants in VCF via picard?
What is the fastest way of getting the total number of variants in a VCF file? (using picard-tools-1.119, via SplitVcfs.jar.) So far the fastest way I could have done it was this: private static int...
View ArticleEmpty vcf when generating PON with MuTect2
Hi, First, sorry if it's a duplicate question. I have looked for solution, but didn't find. I have 8 exomes data from 4 patient: normal and tumor. I ran MuTect2 (in GTAK 3.7) in normal/tumor mode, and...
View ArticleShould I provide the exome target list (-L argu) even while calling gVCF file...
Hi, Recently we performed exome sequencing using Nextera Illumina platform for three samples (Father, Mother and Son). I downloaded the exome interval list from Illumina's website. 1) Trimmed the raw...
View ArticleREGARDING COMBINING VARIANTS IN CLOUDMAP IN GALAXY
Hi I am new to sequencing and i tried with galaxy i am done with vcf files of all mutants and now i have to combine variants but its showing error the tool is as follows...
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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 ArticleSelectively eliminating a set of chromosomes per sample in a multisample VCF
Hello, In my multisample VCF file, some samples have aneuploid chromosome numbers. For example, Sample1 might be 2N for chr1, chr2, and chr3. Sample2, however, might be 2N for chr1 and chr3, but 3N for...
View ArticleVCF - Combining two columns into one column
I have a VCF file with multiple samples (multiple columns). There are replicate samples. Essentially, I want to combine two columns into one. The GT:AD:DP:GQ:PL data would obviously have to be...
View ArticleProblemm with hard filtering
Hi All, I am trying to use GATK for variant filtration (hard filtering) for non human species, using the below command after choosing SNPs only: java -d64 -Xmx48g -jar...
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