GenotypeGVCFs - Best genotyping strategy for trios
Hi the team, I am studying de novo variants in trios (child, father, mother). I used a classical pipeline HaplotypeCaller (GVCF mode)/GenotypeGVCFs, and used about 30 BAMs to perform the genotyping....
View ArticleAway workshop (Gent) 2015 Dec 8: Variant discovery in RNAseq with GATK
The hands-on tutorial files and presentations slides from the Dec 8, 2015 workshop at VIB in Gent, Belgium are available at this link: https://drive.google.com/folderview?id=0BwTg3aXzGxEDb2hTWERNWHg3c2M
View ArticleCalculating allele frequencies in pooled samples
I am resequencing a sample extracted from an aliquot taken from an evolved population, and am looking for a tool that will 1) call variants, both snps and indels, that are at low allele frequency...
View Article--activeRegionIn argument nonfunctional
I've been trying to do some manual adjustments of active regions by running HaplotypeCaller with the --justDetermineActiveRegions option, reading in and adjusting the active region output, and then...
View ArticleRunning ContEst on paired samples -- B:genotype,vcf
I have paired samples of tumor, and normal. I have identified germline mutations from normal sample, and somatic mutations from the pair. Now, I would like to run ContEst on both tumor and normal...
View ArticleRead groups
There is no formal definition of what is a read group, but in practice, this term refers to a set of reads that were generated from a single run of a sequencing instrument. In the simple case where a...
View ArticleI get very different MQ values when using GVCF vs BP_RESOLUTION
Hello! I had a question about the difference between using HaplotypeCaller's --emitRefConfidence GVCF vs BP_RESOLUTION. Maybe the answer is obvious or in the forum somewhere already but I couldn't spot...
View ArticlePicard IlluminaBasecallsToSam: LIBRARY_PARAM file does not have column...
Hi, I am following the GATK pipeline and after running Picard CheckIlluminaDirectory and ExtractIlluminaBarcodes successfully, I encounter a problem to generate the BAM files with Illumina...
View Article(howto) Install all software packages required to follow the GATK Best...
Objective Install all software packages required to follow the GATK Best Practices. Prerequisites To follow these instructions, you will need to have a basic understanding of the meaning of the...
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Which datasets should I use for reviewing or benchmarking purposes?
New WGS and WEx CEU trio BAM files We have sequenced at the Broad Institute and released to the 1000 Genomes Project the following datasets for the three members of the CEU trio (NA12878, NA12891 and...
View ArticleGATK UnifiedGenotyper freeze when run by Java application
Hello, I have a simple run.sh bash script which runs gatk UnifiedGenotyper on 40 bam files. If I run the script manually, analysis finish without problem. If I start the analysis through Java script...
View ArticlePhaseByTransmission reassigns genotype code that conflicts with the allelic...
I encountered a problem running PhaseByTransmission (PBT) module on female proband with both healthy parents. Prior to running the module, the correct genotype was assigned to the Father but after...
View ArticleGATK without swap usage
Hi, I asked a recent question about using picardtools on a cluster with strict swap limits, now I've moved onto using the indelrealigner tool in GATK. My issue is that if GATK starts using the swap, it...
View ArticleInsert size out of range
Hi, I am running picard to sort sam file generated from bwa mem. But I got errors as the following lines show. Could you please help me in solving this problem? Thank you very much. Hui Liu java -jar...
View Articlemore 512M chromosome problem in GATK
i use GATK to deal with Wheat_survey genome which have a 3B chromosome(700+M), it can`t call snp from 512M to 700M use default paramaters, how fix it???
View ArticleVariantEval "stuck" on 1 position
Hi there As in title, i am observing that VariantEval would get stuck in a given position for a very very long time (so long my job on a cluster would get cancelled). I've checked and it is not an...
View ArticleStatistical methods: Inbreeding Coefficient
Overview Although the name Inbreeding Coefficient suggests it is a measure of inbreeding, Inbreeding Coefficient measures the excess heterozygosity at a variant site. It can be used as a proxy for poor...
View ArticleCaller input_prior option
I'm using HaplotypeCaller (but it could be also possible to use this option with UnifiedGenotyper) for a very special experimental design in a no-human species, where we have an expectation for the...
View ArticleGKL 0.3.0
Are there any potential problems/risks to replace gkl-0.1.2 with gkl-0.3.0 (http://central.maven.org/maven2/com/intel/gkl/gkl/0.3.0/gkl-0.3.0.jar)?
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