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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Is it possible to determine the genomic context of a gene in a Whole Genome Shotgun project?

After performing BLAST searches, I 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 gene Y ...
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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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Finding difference between groups

I have mutational catalogues of 4 samples like below ...
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71 views

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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Joining columns to a sorted file

I have had a segmentation file (copy number) like below ...
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43 views

What does this statement mean?

I have a copy number segment file with this by SCAT R package ...
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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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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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Helping with some definitions

In Strelka vcf in INFO column we have these ...
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99 views

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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Merging matched parts of two dataframes

I have a big data frame like this ...
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Interpreting time of clonal divergence in cancer

I am struggling to interpret parts of a figure in this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453324/ In figure 1 parts G and H, they discuses the ...
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1answer
35 views

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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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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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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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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Finding matched genes for each genomic range

I have called structural variants and now I have ...
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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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144 views

Extracting the number SNP in each range

I have called copy number and I have 2 files (I have shared the link of my files ); One contains some ranges ...
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154 views

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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180 views

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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111 views

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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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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Permanent error with picard

I am sure I set the path right but whatever I am trying the command not working Any help please? ...
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327 views

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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Which gene I should select from this qqplot

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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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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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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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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184 views

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 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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102 views

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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839 views

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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266 views

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?