Minor 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 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...
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...
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VCF - Variant Call Format
This document describes "regular" VCF files produced for GERMLINE short variant (SNP and indel) calls (e.g. by HaplotypeCaller in "normal" mode and by GenotypeGVCFs). For information on the special...
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
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...
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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 ArticleCan HaplotypeCaller be used on drug treated samples?
Hello, I am working on a RNASeq data which consists of liver samples from donors. It is a case-control study where 12 samples are divided as Normal (control) and Rifampin Treated (case). I want to...
View ArticleConvert CombineVariant output to individual vcf files
HI, I was curious if it possible to convert the output of CombineVariants back into individual sample vcf files. Based on answered questions in other threads, I am under the impression that you should...
View Articlewhat reads from original BAM are listed in mutect2 VCF-output?
Dear GATK team, I am sorry if my question is naive. After running mutect2 (version 4.2) what positions (AND corresponding reads) from the original bam-file are reported in the vcf file? all that passed...
View ArticleCalculateMixingFractions Returns all NaN?
Hi there, I'm attempting to use the CalculateMixingFractions tool to estimate the mixture of genomes from a VCF in a pooled BAM file and getting all NaN as output. The output looks like this: SAMPLE...
View ArticleVariantRecalibration step issue
Hi all, i need some advice about VariantRecalibration as in if I am doing the right thing? Downloaded 30 bams from 1000 genomes and realigned them to HG38. Then using HaplotypeCaller generated a gVCF...
View Article[INSTALLTEST] Discovery.sh --> VCF is missing
Hi everyone I tried to launch the install test script (discovery.sh). All seems to work : no error in the logs, no error in the stderr. But at the end, I have this message : INFO 10:29:26,082...
View ArticleCombine Variants throwing a bug error
@Geraldine_VdAuwera @Sheila @shlee I am having this issue while merging several single-sample VCF's into a single multisample VCF. CombineVariants is throwing a bug error message $ java -jar -Xmx6g...
View ArticleFrom one sample to multiple samples
I wrote a script in WDL that does 4 tasks to analyze the samples starting from Fastq files until getting a raw VCF file. The script can handle one sample only per time and I wonder if there is any way...
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Standard practice for VCF filtering for the purpose of fingerprinting via...
Hi all, I was wondering whether I could get some insight into what the standard procedure for `fingerprinting' by prop. IBS for sequencing data is. To be more precise: the proportion IBS between the...
View ArticleFilterMutectCalls change between 4.0.2.1 and 4.0.3.0
I tried running FilterMutectCalls on a VCF generated with Mutect2 for matched tumor-normal samples. With 4.0.2.1, I get some variants that are labeled PASS as would be expected, but with 4.0.3.0, I get...
View ArticleVCF to fasta format question
I'm trying to take a multi-sample vcf and convert it to an aligned fasta file for phylogenetic analysis, including all indels and invariant sites. Previous questions similar to this suggested isolating...
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