MuTect2 high insertion counts?
Hi Folks I am using Mutect2 to analyze blood vs. FFPE tumor samples (breast cancer). I am getting (what I think are) unusually high insertion:SNV ratios - the ratio is between 2:1 and 3:1, thus high...
View ArticleSelecting variants of interest from a callset
This document describes why you might want to extract a subset of variants from a callset and how you would achieve this. Often, a VCF containing many samples and/or variants will need to be subset in...
View ArticleGATK best practices pipelinee written in scala for Queue
Hello, I tried to GATK haplotypeCaller, but it is too slow on my WGS data. I have been reading the GATK forums and am trying out Queue to make the pipeline faster. I have gotten as far as the...
View ArticleMutect2 does not support parallel execution with nt
Hi. I ran Mutect2 with the folowing options in a perl script: java -Xmx4g -jar /alloc/sinnett/COMMUN/analyses/TEST/SOFTWARES/GenomeAnalysisTK.jar \ -T MuTect2 \ -R $ref_genome \ -I:tumor $infileT \...
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PhaseByTransmission : Only mendelian violations
I ran PhaseByTransmission and the output is just unphased genotype (except when mother's genotype is missing and newborn homozygotes or the opposite). I used MendelianViolationsFile option and here is...
View ArticleFastaAlternateReferenceMaker gives the input sequence back without applying...
Dear all, I have sequencing reads (mapped with tophat/bowtie2 to reference genome) and from those created vcf files using samtools. Now I have tried to get the fasta nucleotide sequence of a certain...
View ArticleHaplotypeCaller generates diff results on different CPUs
I encountered an interesting problem: running HaplotypeCaller on different machines generates different result for 2 sites. The machines use the same input BAM file, same reference, same java...
View ArticleOut of memory in CombineGVCFs
GATK Team, I am currently attempting to perform a hierarchical merge of gVCF files to obtain a single gVCF containing ~10,000 samples. I've successfully merged the individual gVCFs to 64 gVCFs, but...
View ArticleHaplotypeCaller - Genotype Given Allele Mode
Hi Team, I want to call variants for some samples using Genotype Given Allele mode(GGA) of HaplotypeCaller. I have used UnifiedGenotyper earlier in GGA mode. I am not sure about the right approach to...
View ArticleMergeBam giving error although the inputs are sprted
I am trying to use picard merge bam, after I sort the alignments and unaligned reads wrt queryname using picard. I merge them with SORT_ORDER=queryname Then I get the following error: Exception merging...
View ArticleDo I need to recreate a BAM index (BAI) after running a file through Picard's...
I was running a BAM file through CollectMultipleMetrics and the following exception what thrown: Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record...
View ArticleGenotypeGVCF Parallelism
Hello, I am trying to do joint genotyping with GenotypeGVCF on about 250 exomes. I tried to look at the docs to see the best way to paralyze this process, but didn't find a clear answer. Are nt and nct...
View ArticleMuTect2 in consistence when treat one sample as tumour and normal
Hi, I have mouse cell lines which have been treated by PGDF. Some of the cell lines turned into tumor, some didn't. When I was using MuTect2 call SNP and Indels for the sample which are not turned into...
View Articlevariation info found in bam but not in final vcf file
Why veiw the bam by samtools, there is snp variation on one position,but in the final vcf file, there is no variation result on that position. please kindly see the following sample NA12878-580ng-2 for...
View ArticleGATK RUNTIME ERROR (version 3.6-0-g89b7209) running HaplotypeCaller single...
Hi, Following "best practice", I am running haplotypecaller for each individual with the command java -Xmx131072m -jar GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -I bam \ -o g.vcf \ -R...
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Variant Quality Score Recalibration (VQSR)
This document describes what Variant Quality Score Recalibration (VQSR) is designed to do, and outlines how it works under the hood. The first section is a high-level overview aimed at non-specialists....
View ArticleVariantFiltration WARN and not working
Hello, I am in the process of hard filtering my SNPs (non model species, 85 whole-genomes, GATK' best practices pipeline). After removing multiallelic SNPs with SelectVariant, I already applied...
View ArticlegVCF Backwards Compatibility?
I have a series of gVCF files all generated since around April. I recently ran GenotypeGVFs to call genotypes on a set that included 21 files, 19 "old" and 2 new (generated this week). The resulting...
View ArticleNot all FORMAT fields are being emitted
I' am using the CombineVariants tool from GATK after calling mutations with Mutect. To simplify my case I will show three samples and one variants. Specifically, I encounter the problem where for the...
View ArticleQuestions about GenomeSTRiP
Hello, I have a question about software GenomeStrip. Cloud you please tell me if there were metadata bundle for hg38? Thank you very much.
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