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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How to subset samples from a VCF file?
I have VCF files (SNPs & indels) for WGS on 100 samples, but I want to only use a specific subset of 10 of the samples. Is there a relatively easy way to pull out only the 10 samples, while still ...
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Tumor purity/contamination/admixture estimation
Can anyone recommend a good tool for estimating the tumor content given a matched tumor and normal file for DNA NGS whole genome sequencing data or whole exome data?
Is it possible to estimate this ...
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How to compare groups using WGS data?
We have whole genome sequencing data for patients (not-cancer) (n=60) and for healthy controls (n=20). The sequencing centre has provided us with the best practice bioinformatics analyses including ...
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Which tools can detect chimeric RNA (fusion genes) from WGS or RNA-Seq data?
Given WGS data or RNA-seq data, which tools can I use to detect gene fusions?
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How to compare 2 whole genome sequences [closed]
I have the files of 2 persons that got whole genome sequencing, one by nebula genomics and the other by dante labs.
I want to compare their genomes to see if they are father and son.
I want to see ...
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GATK documentation for required depth to reliably call heterozygous mutation in diploid organism?
I'm looking for official GATK documentation (or a recent manuscript) that defines a general recommendation/requirement for sequencing depth to reliably call a heterozygous point mutation in a diploid ...
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Plot percentage of genome covered
Given a aligned bam file (wgs/bwa-mem) what steps do i need to perform to generate a plot as seen below (from this paper):
We are trying to see how much of genome was covered using pacbio and ...
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Where can I get the population allele frequency vcf file?
I want to use GATK to estimate cross-sample contamination for Whole Genome Sequencing data.
The specific tool is ContEst and it is run with:
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Which gene I should select from this qqplot [closed]
I have a qqplot of my whole genome sequencing data; A plot is for showing possibly significant driver genes. I tried to read about qqplot though but people only say about the skewedness while I want ...
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Is there an alternative to bulked segregant analysis for insects?
This strategy seems to be most commonly used for plants. When crossing animals isn't possible, how can I do a similar study to identify a particular locus responsible for a polymorphic trait (...
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How to find all WGS assemblies accessions of a species
Some background
Similar to the OP of https://www.biostars.org/p/377840/, I would like to programmatically BLAST a sequence to a local database of all WGS assemblies.
Since this isn't feasible for the ...
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Variant calling without matched normal sample
I have WGS .bam files for 3 patients (tumour and its matched derived model namely organoid) but I don't matched normal sample. If I call variants of each patients (tumour and its matched organoid), ...
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Obtaining Whole Genetic Sequence
As an end-user of my own data, specifically raw DNA sequence (WGS, whole genome sequencing). How or where do one obtain such DNA data so that a biology hobbyist can perform bioinformatics on this?
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Can we test the accuracy of Phred scores shown in FASTQ files
Recently I have ran a human WGS on the BGI DNBSEQ system, and their FASTQ quality scores seem to be quite impressive, where the Phred scores barely deteriorate along the read length when checked on ...
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Why might parabricks not be writing output to the output file I provided?
This feels like a silly question, but I am testing parabricks bammetrics and nothing is being written to my output file. This is the command I am using:
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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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What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?
(I am not a Bioinformatics expert, please forgive and educate me if I've used any wrong terms or assumptions here)
I bought a "Whole Genome Sequence" kit, which gave me the following VCF ...
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What does this statement mean?
I have a copy number segment file with this by SCAT R package
...
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Where can I download 30x 1000 genomes cram files?
From the preprint published by 1000 genome project (https://www.biorxiv.org/content/10.1101/2021.02.06.430068v1.full) I think the 30x data is for WGS. Can anyone confirm for me if the following file ...
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Help with the definitions of fields in a VCF output by Strelka
In Strelka vcf in INFO column we have these
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Common QC parameters and threshold in human WGS pipeline
I am trying to summarize a list of QC-parameters and its threshold that should be applied for human WGS in general to avoid bad quality of data.
Which qc parameters for WGS are you using and why?
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Plink 1.9 --merge-list changing order of fam file
I am doing some whole-genome sequence analysis and to speed things up split the data into chromosomes and also into regions within those chromosomes. (So I have my dataset split into ~300ish files) I ...
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How to align multiple contigs? To generate full length genome
I have MAG geneome sequence released in NCBI. In the released sequence there are 4915 contigs present. I want to get the full length genome sequence as FASTA file to proceed with further works like ...
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MetaQuast for assembling samples from complex communities
I'm working with whole genome metagenomic samples from human skin, and I'm using MEGAHIT for assembly and MetaQuast for evaluation. However, MetaQuast requires a list of reference genomes for the ...
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What does these terms mean?
I am working on cancer genomics failed to follow some terms even by googling
What is the difference of focal genome amplifications versus convergent amplification of given region of genome for ...
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GATK 4.1.4.0 Mutect stats output
I have adapted my pipeline to the new filtering strategies implemented in gatk 4.1.4.0 and while looking at its output I noticed that the stat file generated by mutect2 has a negative number:
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Sibling vs Parent/Child relationship detection using whole-genome sequence data
I am analyzing a family-based whole-genome sequence (WGS) dataset. My identity-by-descent(IBD) analysis shows they share about 50% of their DNA. I think my pedigree structure may have gotten mixed up ...
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Which tools are available to call somatic mutations on non-coding regions from whole genome sequencing data?
I have a set of whole genome sequencing samples, some of which have matched normal while some not. I want to call somatic mutations on non-coding regions.
I was looking for GATK best practices (like ...
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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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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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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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Getting this information for GISTIC2
Long time I am struggling how to provide GISTIC2 required input like Num_Probes and Segment_Mean
I have called somatic copy ...
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Variant calling for a subset of genes using whole gneome sequencing data
I have few 100 raw fastq files from whole-genome sequencing data and I would like to map these files to a set of genes only (and not whole genome) so as to find SNP's associated with them. Can anyone ...
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Looping over several files in bash
I have a bash script:
I am wondering how I can change this script to loop over a bunch of .vcf files and give output .txt with the name of corresponding .vcf
I tried changes done in similar script ...
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Best practice for running GATK VQSR on X chromosome
According to GATK best practice, it is recommended that different VQSR models be built for SNPs and INDELs, because the annotations for high-quality SNPs and INDELs are systematically different (if I ...
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Generate table for total number of SV events per sample
I have called and annotated structural variants and I have a table by name of samples and structural events like below
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Parsing .vcf file for this information
I have a .vcf file
https://www.dropbox.com/s/8v73nppwg3a1tnd/LP2000109-DNA_A01_vs_LP2000103-DNA_A01.SVannotated.txt?dl=0
with this header
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Assemble Anaeroplasma species genome from metagenomic PacBio data
I have a fasta file containing reads generated by PacBio HiFi whole genome sequencing of a feces sample from mouse.
I would like to use this dataset to generate an assembled circularized genome for an ...
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polidy VCF file for Canvas somatic-wgs cnv calling
I am trying to run Illumina CANVAS cnv caller for Somatic-WGS. There is an option "--ploidy-vcf" which is mandatory to supply, but don't know what exactly that mean. I had supplied the CNV....
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Plot a circos plot to show the consistency between 2 samples
I have called SNP and INDEL in two matched samples by strelka and extract this information from .vcf file and I have these
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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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Picard validation error regarding bin field of BAM file
I am sure I set the path right but whatever I am trying the command not working
Any help please?
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Making a boxplot or violinplot for several dataframe with different number of samples
I have 3 data frames for treatment of 3 different drugs and in each of them I have the number of mutation types like insertion, deletion, SNP and total of mutations for each patients. In each group I ...
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Removing common variants in the 1000 genomes database from .vcf [closed]
I have 15 .vcf files. I need to remove `common variants in the 1000 genomes database' appearing in at least 0.5% of the population
Do you know from where I may start?
Thank you so much
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Finding matched genes for each genomic range
I have called structural variants and now I have
...
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