HaplotypeCaller Error: SAM/BAM/CRAM Invalid GZIP header
This is my GATK (3.5-0-g36282e4) arguments Program Args: -T HaplotypeCaller -R human_g1k_v37.22.fasta -nct 16 -I ref.22.500x.bwamem.sorted.bqsr.bam -I somatic_sim_af20_500x.bwamem.bqsr.bam -I...
View ArticleGATK 3.8: Allele-specific Annotations
I am using GATK-3.8.1 for HaplotypeCaller (using gVCF mode and then GenotypeGVCF) and I noticed that final VCF output from GenotypeGVCF has missing DP values. I found a workaround that while doing gVCF...
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(How to) generate a complete realigned bam file using -bamout argument in...
Hello, I want to get a realigned bam file for other tools to call variants, so I used the -bamout argument in HaplotypeCaller. I found that bam file is incomplete when I used only -bamout argument....
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...
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HaplotypeCaller: Alternate allele get called or not depending on -ip option
Hi, I'm currently analyzing some data (exome-seq) using HaplotypeCaller and get what seems to me an odd behaviour: The problem is that I've got a position which is clearly bi-allelic in IGV and that is...
View ArticlePhased Heterozygous SNP
Dear all, I have difficulties in understanding the genotypes of the phased SNPs. Here i have a SNP where only one read has a reference allele and 11 reads have an alternate allele and is called as...
View ArticleIs there a paper describing the »Haplotype Caller algorithm?
Hi, I'd like to ask you if there is a paper describing the Haplotype Caller algorithm, if you could please send me the reference. I have tried to find it, but I only found the paper on GATK which is...
View ArticleHaplotypeCaller sensitivity in large(ish) cohorts
One of my projects currently has ~150 patients (exomes) that I've been processing through the standard pipeline (2.8-1, including ReduceReads). In my most recent run through HC, I split the cohort in...
View ArticleAllele Depth (AD) / Allele Balance (AB) Filtering in GATK 4
Hi, I am trying to filter my GATK 4.0.3 - HaplotypeCaller generated multi-sample VCF for allele depth (AD) annotation at sample genotype-level (so available in "FORMAT" fields of each sample). I think...
View ArticleGenotypeGVCFs and VariantFiltration tools
We are following "Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode" best practices using GATK 3.8.1 and Java 1.8. Thus we merged the raw.g.vcfs from HaplotypeCaller into...
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GATK HaplotypeCaller missing SNPs at the terminals of the segment when...
We are trying to call variants for Influenza A virus sequenced by MiSeq using HaplotypeCaller following GATK best practices (GATK version 3.7). However, when checking in IGV the called variants with...
View ArticleUsing NIO with GATK4 HaplotypeCaller
Is GATK4 HaplotypeCaller NIO compatible? If not, is there another version that is? Thanks!
View Articlei am running haplotypcaller in one bam file
java -jar GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T HaplotypeCaller -R reference/GRCh37/hs37d5.fa -I output.bam --dbsnp reference/gatkbundle/dbsnp_138.b37.vcf -o output.g.vcf -ERC GVCF i am trying...
View ArticleSNP calling using pooled RNA-seq data
Hello, First of all, thank you for your detailed best practice pipeline for SNP calling from RNA-seq data. I have pooled RNA seq data which I need to call SNP from. Each library consists of a pooled...
View Article"UKNOWN" zygosity in CSV file
Hi There, I am using GATK 3 . Recently i checked two CSV and bam file for couple, that both of them are carrier of one pathogenic variant, But in CSV file, the zygosity of this variant in both of them...
View ArticleIs UnifiedGenotyper actually better than HaplotypeCaller for this pooled...
Hi, I am interested in calling variants from pooled samples. Specifically, I wish to determine SNP allele frequencies from samples that were made by pooling many individuals (1000+) together. I know...
View ArticleHaplotypeCaller gives error and generate vcd file with no variant call
Dear GATK Team, I'm using GATK and picard to call short variant from plasmodium genome paired read fastq file . I used the HaplotypeCaller package after doing duplicate marking using picard...
View ArticleCalling invaiant sites with the new pipeline of HaplotypeCaller
Hello, I am using the new pipeline of haplotype caller in order to obtain a vcf file containing both variant and invariant sites. For each individual, I called variant and invariant sites : java...
View ArticleAll annotations in BP_RESOLUTION mode
Hello, I was wondering if there is a way to output all annotations for all sites when running HaplotypeCaller with BP_RESOLUTION. Currently it outputs all annotations for only called variants. Thanks...
View ArticleHaplotypeCaller output header and one position recode without error
I'm trying to run gatk4 HaplotypeCaller using the following command: ./gatk HaplotypeCaller -R ./reference.fasta --emit-ref-confidence GVCF --dbsnp ./samtools_gatk_common.vcf -I ./sample.bqsr.bam -O...
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