Adding dbSNP rs identifiers to VCF files
Dear GATK team, I produced VCF files from RNA-Seq data as described in https://www.broadinstitute.org/gatk/guide/article?id=3891 My VCF files contain genomic coordinates but not dbSNP rs IDs. Is this...
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 ArticleWhat are the recommendations of VariantFiltration for variants derived by...
I have 23 samples and I want to look over 63807197 bp region. Many thanks before. Kind regards, Angelica
View Articlesame setting, different results (GATK...
When I run GATK with identical settings on some amplicon sequencing data from MiSeq (150KB region), I get different numbers of variants (approximately 10% difference), even after setting -dfrac to 1....
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GATK version 3.2-2 - possible bug
Hi, I had called a VCF using haplotypecaller, following general guidelines with the GATK version 3.2-2. I had encountered a possible bug where a sample is shown to have a HET genotype, yet the AD...
View ArticleHomozygous SNP
Hi, I have the below variant from GATK Haplotype caller and annotated as 1/1 which means homozygous for the alternate allele. chr1 10023229 . G A 101.03 ....
View Articlewhat does this ERROR mean - "Problem detecting index type"
I ran GenotypeGVCFs on all the vcf files generated by HC using the following command ( All these file are indexed by HC): java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R /ref/human_g1k_v37.fasta -o...
View ArticleGenotypeGVCFs hangs on some positions
Hi all, I am attempting to use the HaplotyperCaller / CombineGVCFs / GenotypeGVCFs to call variants on chrom X and Y of 769 samples (356 males, 413 females) sequenced at 12x coverage (WG sequening, but...
View ArticleParameter to set the min-freq
Hi, Is there any parameter to set the minimum variant frequency? What is the parameters name? I have read the documentation, but I cannot find it. Thank you,
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 ArticleDoes the Haplotype Caller perform Linkage Disequilibirum as part of the...
Hi, I'd like to know if the Haplotype Caller perform Linkage Disequilibirum (LD) to decide wether to call a variant or not as part of the variant callling algorithm? I've read documentation about the...
View ArticleWhy is HaplotypeCaller dropping half of my reads?
Hi I have been trying HaplotypeCaller to find SNPs and INDELS in viral read data (haploid) but am finding that it throws away around half of my reads and I don't understand why. A small proportion (8%)...
View ArticleHaplotypeCaller SB field for multiple-alts
The SB field of HaplotypeCaller output is not described terribly well as far as I can find. ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the...
View ArticleSplit joint variants-calling files into SNP and Indel
Hi. I used haplotypecaller for variants calling. After variant recalibration, there is a vcf contains both SNP and Indel. Is there any quick way to split it into two vcf: SNP and Indel. Thanks. Lei
View ArticleHaplotypeCaller 3.3-0 Homozygous variant calls
Hi, I just finished running HaplotypeCaller version 3.3-0 separately on 6 exome samples with the new best practices. java -Xmx8g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19/hg19_Ordered.fa -I...
View Articlehaplotypecaller with VectorLoglessPairHMM without speedup.
Hi team! I am testing haplotypecaller with VectorLoglessPairHMM on a singel BAM. There are two weird things. There is no speedup going from -nct 1 to -nct 10. There is no speedup implementing...
View ArticleEffect of performing RNA-Seq with a highly fragmented reference genome:...
Hi, I am performing RNA-Seq to identify new polymorphisms in a species of sea star. Our short-term goal is to generate novel DNA sequences of coding genes for phylogenetic analysis. It is therefore...
View ArticleCalling complex pedigrees with HaplotypeCaller
Hi, I want to use HaplotypeCaller to call families together. I have bam files for each individual in the 4 families I am studying, as well as a ped file describing the pedigree information. The problem...
View ArticleArguments for HaplotypeCaller or GenotypeGVCFs
If I want the variants to be called only if they fit the following criteria: 1) Min. total coverage for consideration of heterozygous is 10. 2) Min. coverage of each of the two observed major basecalls...
View ArticleWhat exactly does the --minReadsPerAlignmentStart flag specify in...
Specifically, what does the 'start' component of this flag mean? Do the reads all have to start in exactly the same location? Alternatively, does the flag specify the total number of reads that must...
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