GATK FilterVariantTranches - all mutations passed the filter

Hi, Biostars community.

I tried to filter variants in my .vcf file using GATK CNNScoreVariants and FilterVariantTranches, but in result file all mutations passed the filter.

Commands:

gatk CNNScoreVariants -V input.vcf -R reference.fa -O scored.vcf

gatk FilterVariantTranches -V scored.vcf \
   --resource hapmap_3.3.hg38.scored.vcf \
   --resource Mills_and_1000G_gold_standard.indels.hg38.scored.vcf \
   --info-key CNN_1D \
   -O result.vcf

Addictional info:

GATK version: 4.1.8.0
OS: Ubuntu Server 18.04
All commands executed under GATK conda enviroment.
Resource vcf files scored via CNNScoreVariants.

Solved

Solved via specifying "-snp-tranche" and "-indel-tranche" options.

gatk cnnscorevariants filtervarianttranches

• 1,841 views • link

written 6.0 years ago by Vladislav •

0 answers

No answers yet.

More posts like this

A USER ERROR has occurred: Bad input: Values for QD annotation not detected for ANY training varian…
written 2.0 years ago by sam_brown_araujo •

Hi all, I have been having issues using VariantRecalibrator in GATK 4.4.0.0. My command is: gatk VariantRecalibrator \ -R {ref.fasta} -V {input.vcf.gz} \ --resource:hapmap,known=false,training=true,truth=true,prior=15.0 {path/to/vcf.gz} …
VQSR first step do not generating plots
written 3.5 years ago by Yoosef •

Hello. After running my codes for VQSR's first step, I receive all files (including R scripte for plots) except the pdf file that contains plots. …
Padding out a GVCF file with 1000G exomes to get gatk VariantRecalibrator working with a small samp…
written 4.7 years ago by michael.flower.14 •

I've got sequencing data for a small 500 bp amplicon from a few samples. GATK best principles suggest running [VariantRecalibrator][1] on the GVCF files I …
So many variants detected.
written 5.0 years ago by Mehmet

Dear All, I have done variant calling in Germline data that has single sample of each individual and two genes. I did following steps, but …
no variant remained after GenotypeGVCFs gatk4
written 5.0 years ago by Mehmet

Dear all, I am analyzing a DNA-seq data to identify variants in two genes of human using a single-sample based gatk4 pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-). Haplotypecaller identified …
ReadPosRankSum annotation error (gatk4)
written 6.3 years ago by Cricket •

Hello. I am using GATK 4.1.3.0 to filter variants according to the VQSR steps listed here: [How to Filter variants with VQSR ][1]. I am …
random selection of multi-sample vcf does not work
written 7.0 years ago by mernster •

Hey there, I am trying to randomly select variants from a multisample vcf file which I generated by merging several individual vcf files together using …
GATK4: an error with VariantRecalibrator
written 7.3 years ago by tongshiyuan •

Hi, I use the VariantRecalibrator with GATK-4.0.10.1, and my sample is WGS data. I use CombineGVCFs with trio. it make an error: 18:19:38.004 WARN VariantDataManager …
QD Annotation error in GATK in VariantRecalibration step
written 8.5 years ago by win

hi all, i downloaded a BAM file from 1000 genomes to work on and converted it to FASTQ and aligned with bwa mem to hg38, …
WGS data for pipeline development
written 8.5 years ago by win

Hi all, i am looking for paired end Illumina FASTA files from whole genome NGS run. I am developing some pipelines and was using a …