Questions tagged [wgs]

Whole genome sequencing. Can refer to sequencing that is done on the entire genomic DNA, as opposed to techniques that only sequence a subset of the genome, like ChIP, RAD-seq or exome sequencing.

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Different ClinVar classifications/SNPs are linked to the same rsid

I am using R to extract ClinVar classification of SNPs using rsid. Here's an example of my workflow: Patient data: Sample Func Gene Codon_Change dbSNPv151_GRCh38 Chr Start End Ref Obs Mary ...
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CNVKit does not output all the accessible regions in the targets bed file

This question was also asked on Biostars I am using CNVkit on my data using hg38 as reference. The command that I am using is the following: ...
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About workflow input section in DRAGEN-GATK v1 whole genome analysis script

I am trying to understand the WDL script for the DRAGEN-GATK whole genome analysis and I am faced with this input section inside the workflow definition which I really don't get: ...
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Confusion about GISTIC threshold

Please, can you help me with a confusion? In whole genome sequencing, if Total copy number (major + minor allele copy number by SCAT R package) for SMAD4 in a ...
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tabix to subset each VCF by the coordinates given

I have a vcf file like below ...
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Are there any simple ways to call copy number variants from a Nebula Genomics WGS data?

I want to find my copy number variants. I got DNA testing from the Nebula Genomics and received the raw datas in .cram, .fastq, .vcf formats. Are there any simple and easy method to call my copy ...
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Compare illumina sequencing output with reference genome

I am new to whole genome sequencing. I want to compare illumina whole genome sequencing of mutants of a particular bacteria with a genome (not annotated) of the original strain to look for what the ...
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Is it possible to determine the genomic context of a gene in a Whole Genome Shotgun project?

I performed several BLAST searches and identified several genes of interest in a Whole Genome Shotgun (wgs) project. I know that gene X is located on scaffold 1234, from nucleotide 1 - 2250, while ...
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How to choose reference to calculate coverage of WGS of organism that has high intra-species variation?

Calculation of coverage involves mapping reads with a reference and depending on the choice of reference we can get very different result. If a species has a genome that has very low size variation ...
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Fastest way to count where two bam files are homozygote reference (inverted variant calling)

Maybe I'm having a brain-freeze so excuse me if this is a waste of everyone's time... I am working with an organism with ~700Mb genome. I have bam files of two individuals that are whole genome ...
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