GenotypeGVCFs 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...
View ArticleUsing NIO with GATK4 HaplotypeCaller
Is GATK4 HaplotypeCaller NIO compatible? If not, is there another version that is? Thanks!
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 warnings DepthPerSampleHC
Hi I'm trying to do a multisample variant call using several bam files in the following cmd /mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk HaplotypeCaller -R /mnt/fastdata/md1jale/reference/hs37d5.fa...
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 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 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 Articlei_variant_quality_by_depth/i_genotype_quality interpretation
When interpreting the output of HaplotypeCaller, what do the i_variant_quality_by_depth and i_genotype_quality columns represent and which of these would be a good value on which to base an assessment...
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...
View Articlea question about running HaplotypeCaller with intervals
Hi, I have a question when running HaplotypeCaller functions with intervals on exome-seq data. Here is the command I used: java -jar gatk-package-4.0.6.0-local.jar HaplotypeCaller -R...
View Articlecan VariantsToTable output the raw genotype call (i.e., 0/1) rather than the...
I'm interested in getting simple "heterozygous" or "homozygous" designations for all of the samples/SNPs in my multisample VCF file. In the past, I have been using the -GF GT option in VariantsToTable,...
View ArticleShort read data in highly repetitive genomic region for heterozygous individuals
Hello GATK team, This might be a very general and overrated question but I appreciate your input. I am working with natural populations of plants (expected highly heterozygous individuals) and an...
View ArticleDistribution of RGQ scores
I work with non-human genomes and commonly need the confidence of the reference sites, so I was happy to see the inclusion of the RGQ score in the format field of GenotypeGVCFs. However, I am a little...
View ArticleIssue of Haplotype call on a large chromosome (>536 Mb)
Hi I tried to run HaplotypeCaller with GVCF mode. My reference genome is over 5 Gb in size. Below my code and error, Using GATK jar /source/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar Running: java...
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Mutect2 missed variant called by HaplotypeCaller
Hi, I am running GATK 3.5.0 with java version 1.8.0. I have two cell line samples that I paired with a promega baseline reference (its essentially a mixed germline sample) to run Mutect2 (which I am...
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Haptyepecaller calls incorrect genotype in several site
Hi, I found that the Haptyepecaller made heterozygous calls where there is no support for them in the BAM. We use IGV to compare input BAM and Haptyepecaller output bam. The region shown in the figure...
View ArticleQuality of mutation by constructing haplotypes
Hi there, i have two questions one can i construct haplotype using GATK haplotypecaller? how can i check the quality of a mutation using haplotypes?
View ArticleIs there any way to take vcf data and output 2 fastas - one of each of the...
So I looked at using the ReadBackedPhasing tool or the Haplotype caller but I already have a calling pipeline setup that works well with my data and I'm really just looking at a way to leverage the...
View Articleadapter removal and variant calling in samples with different library...
Hi, This question is an amalgamation of good practice and conceptual doubts. So I have a cohort of a non-model organism of say approx. 100 animals. 40 have been sequenced at 10x depth by Illumina 2500...
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