Tag: GenomicsDBImport
How to extract phased haplotypes from GATK HaplotypeCaller
I would like to extract the physically phased haplotypes from a VCF file generated by GATK’s HaplotypeCaller on Illumina data of some isolates from different yeast (S. cerevisiae) strains. According to this FAQ: In the format field of a PGT (Pre-Implantation Genetic Testing) VCF, you may find a description similar…
Whole-genome sequencing reveals an association between small genomic deletions and an increased risk of developing Parkinson’s disease
Case selection In this prospective case‒control study, we enrolled PD patients and healthy controls at Asan Medical Center (AMC), Seoul, South Korea, between 2018 and 2020. PD diagnosis was based on the UK PD Society Brain Bank criteria15. Batch 1 (n = 210) and 2 (n = 100) PD cohorts were recruited from January…
GenomicsDBImport datastore format folder permissions
Bug Report Affected tool(s) or class(es) GenomicsDBImport / GenotypeGVCFs Affected version(s) 4.3.0.0 Description When creating a GenomicsDB datastore, the created folder has permissions set to 700 (recursivelly).As such, when trying to jointly calling genotypes using the GenotypeGVCFs, one encounters error:ERROR: Couldn’t create GenomicsDBFeatureReader Steps to reproduce Create a datastore using…
Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment
Sample preparation We ordered the GIAB samples from the Coriell Institute (NA24385, NIST ID HG002; NA24149, NIST-ID HG003 and NA24143, NIST-ID HG004). DNA concentration was measured by Qubit. The library was constructed according to Illumina TruSeq DNA PCR Free Library Prep protocol HT (Illumina Inc., San Diego, CA, USA) for…
GATK’s GenomicsDBImport takes forever…
GATK’s GenomicsDBImport takes forever… 0 Hello! I have 90 samples in the form of vcf files, together they are a few terabytes in size. I wish to create a single multi-sample vcf file for downstream analysis. I am trying to use GenomicsDBImport for this, but it just takes too long…
Contig chr1 given as location, but this contig isn’t present in the Fasta sequence dictionary
Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn’t present in the Fasta sequence dictionary 2 Hi everyone, I’m trying to run Mutect2 for WES cancer data. However, since their Resource bundle only supports h19 seems I cannot proceed (I want to compare it with Strelka2…
