Joint genotyping using GenotypeGVCFs command line
Dear all, we have set up a bwa + gatk best pratices pipeline for variant calling on exome data. we use the haplotype caller in gvcf mode. my question is how to set up the genotype gvcf module for...
View Articlegenerate an idx file for a vcf
Hello, I have a vcf file that does not have an associated index file. Is it possible to create one? If yes, what module do I need to use? Thanks for your input! ~Mika.
View ArticleHaplotypeCaller on defined set of SNPs
I have a set of sequenced PCR amplicons in bam files (one per samples) where I need to call defined SNP positions to get a combined genotype, no matter if it is reference or alternative homozygous or...
View ArticleHaplotypeCaller what is j in calculation of genotype likelihood?
I have read the Methods and Algorithm section HC step 4: Assigning per-sample genotypes. I follow up until the equation for P(D|G) that includes a product over j. Please explain what j is. Are you...
View ArticleHaplotypeCaller - number of haplotypes/alleles to allow
If I am analysing a single sample, can I specify a lower value for maxNumHaplotypesInPopulation and maxAltAlleles? Should these variables scale with the size of your sample population?
View Articlewhat does the minReadsPerAlignmentStart argument in HaplotypeCaller mean?
The minReadsPerAlignmentStart argument in HaplotypeCaller is described as the minimum number of reads with the same alignment start for each location in an active region and has a default of 10. For...
View ArticleHaplotypeCaller with very low coverage/inconsistent coverage bam file
Hello, I recently had to download some SOLiD datasets (whole genome, non-human) from a paper published in 2010 and perform SNP calling using those reads. I roughly followed the best-practices...
View ArticleAny plan for MuTect2 to support calling more than a single tumor-normal pair...
I would like to be able to compare many samples to each other at a time to find the frequency of somatic SNP appearance across multiple samples. Are there any plans to allow for MuTect2 to make...
View ArticleGenotype Concordance HG19 file? Which to pick?
I'm looking for a standard high confidence VCF file to compare several dozen NA12891 samples for genotype concordance. We are testing different protocols and would like to determine which is most...
View ArticleOncotator reports on error, could you please help?
Hi, I am trying to use Oncotator v1.9.0.0, and receiving the following error. Could you please help me to figure out what to do? some details: I am running Oncotator v1.9.0.0 on a cluster, on anaconda...
View ArticleInstalling latest Mutect1
Hi, To review a paper, I would need to install MuTect.1.1.7 that I got from the GATK download page. GATK3.6 is already installed on my machine but I am not sure if it is compatible with MuTect1. I also...
View ArticleError while running GATK4 CNV workflow (something with the HDF5 lib)
Hi the GATK team, I am a new user of GATK4 CNV workflow. I always had an error while running the 3rd step NormalizeSomaticReadCounts: 16:08:11.670 INFO IntelGKLUtils - Trying to load Intel GKL library...
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Mutect2 dont list Variant
Hi, Iam running mutect2 on capture data, with tumor normal. The data flows the "classic" way on a local wdl-pipeline with bwa =>merge=>markDup=>recal=>mutect2 (3.6). I see the variant...
View ArticleHaplotypeCaller pooled sequence problem
Hi, I have a number of samples that consist of multiple individuals from the same population pooled together, and have been truing to use HaplotypeCaller to call the variants. I have set the (ploidy to...
View ArticleIs PL actually a probability ratio not a likelihood? And consequences for GQ
I read the methods section Math notes: how PL is calculated in HaplotypeCaller which says that PL is based on the probability of the genotype given the data. Does this mean that it includes the product...
View ArticleGenotypeGVCFs --max_genotype_count not working?
Hi, I'm currently trying to call SNPs from a mixture of 42 pooled (a 10 individuas) and 50 individual sequenced chicken, using HaplotypeCaller and GenotypGVCFs (GATK3.7). Using the HaplotypeCaller, the...
View ArticleError running the GATK WDL best practices pipeline
Hello, I am running the GATK WDL best practices pipeline with the sample data from the Google Cloud...
View ArticleRNA-seq variant calling for somatic
I want to find best practice to do variant calling from this page : https://software.broadinstitute.org/gatk/best-practices/ I have exome-seq and RNA-seq data and I think because the sample is from...
View ArticleRNA-SeQC giving Badly formed genome loc error
Hello, I'm trying to run RNA-SeQC by: java -jar RNA-SeQC_v1.1.8.jar -o RNA-SeQC -r ../References/hg19_mt_virus_rDNA.fa -s...
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Problem when running HaplotypeCallerSpark locally
I'm running HaplotypeCallerSpark locally, but I cannot see the progress lines on console, like how it was when running GATK 3. It only shows spark-related information. How can I get the progress report...
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