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 debug a bash script

Please somebody debug my code In sub-folders there are 500000 vcf files from which I only need 500 vcf files listed in ...
1 vote
1 answer
31 views

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 ...
2 votes
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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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tabix to subset each VCF by the coordinates given

I have a vcf file like below ...
15 votes
4 answers
34k views

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 ...
2 votes
1 answer
110 views

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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1 answer
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Can I interpret 15x coverage area as a part of one strand is missing?

This is a BAM file from a 30x coverage Nebula Genomics test opened with IGV. I found an area (1:30169255-30169600) where the coverage is less than 15x. Can I interpret it as a part of one strand of ...
2 votes
2 answers
41 views

Longstitch error make: command: Command not found *** No rule to make target

I installed Longstitch and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error. <...
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Does phasing improve imputation quality?

If so, by about how much? I want to know the downsides of skipping the phasing step on human microarray and WGS data.
3 votes
1 answer
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What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?

I bought a "Whole Genome Sequence" kit, which gave me the following VCF files (this service did not include any analysis, just the raw data): cnv.vcf <...
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1 answer
79 views

Finding difference between groups

I have mutational catalogues of 4 samples like below ...
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1 answer
100 views

obtaining a fragment data file bed from bam

Im trying to follow this pipeline https://github.com/epifluidlab/cragr on cfDNA WGS. I have bam files from paired end reads aligned with bwa mem. The workflow requires bgzipped and indexed fragment ...
2 votes
2 answers
52 views

What would be the best method to obtain every prokaryotic psychrophile genome?

I am interested in running an analysis on the genome of every psychrophilic bacteria. Here defined as bacteria that have an optimal growth temperature at less than 15°C. What would be the best way to ...
1 vote
1 answer
144 views

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 ...
2 votes
1 answer
115 views

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 ...
2 votes
1 answer
122 views

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: ...
1 vote
1 answer
206 views

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 ...
3 votes
1 answer
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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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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 ...
1 vote
1 answer
82 views

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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2 answers
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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 ...
2 votes
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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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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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1 answer
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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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1 answer
248 views

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 ...
6 votes
2 answers
522 views

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 ...
0 votes
2 answers
508 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 ...
2 votes
2 answers
123 views

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? ...
1 vote
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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 ...
3 votes
1 answer
192 views

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 ...
1 vote
1 answer
363 views

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: ...
1 vote
1 answer
327 views

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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1 answer
541 views

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? ...
1 vote
2 answers
123 views

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? ...
2 votes
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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 ...
-2 votes
2 answers
317 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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1 answer
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Joining columns to a sorted file

I have had a segmentation file (copy number) like below ...
1 vote
1 answer
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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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2 answers
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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 ...
-1 votes
2 answers
527 views

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 ...
1 vote
2 answers
74 views

Merging matched parts of two dataframes

I have a big data frame like this ...
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2 answers
208 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 ...
1 vote
1 answer
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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 ...
1 vote
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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 ...
1 vote
1 answer
139 views

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 ...
1 vote
1 answer
495 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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1 answer
109 views

Finding matched genes for each genomic range

I have called structural variants and now I have ...
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1 answer
32 views

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 ...
-9 votes
1 answer
549 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 ...
0 votes
1 answer
309 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 ...