Questions tagged [variation]

Refers to genetic variation such as SNPs, indels, and structural variants within a population or between individuals.

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Is it possible to identify SNP sites that underwent LOH in a cancer sample, without associated normal sample?

I am trying to identify sites that underwent LOH in a cancer sample, but I don't have an associated normal sample. I know population SNP VCFs are available (for example, from 1000G), that can ...
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1 vote
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Benchmarking for variant identification using RNA-seq data

I am in need to benchmark the variant identification pipeline which uses RNA seq data alone without any matched-normal. I would like to know the reference dataset (and the pipeline on which the ...
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2 answers
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Multiple Sequence Alignment

I applied three multiple sequence alignment methods of muscle, mafft and clistal omega on 30 sequences and 400 sequences . In the case of 30 seq, the output of alignment from the 3 methods was in the ...
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1 answer
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Getting all variants in a region from ensembl

I want to get all the variants (SNPs) in a given region of the human genome. Is there a way on how to do this with the ensembl-API? It should be a representation similar to this: There I added dbSNP ...
3 votes
1 answer
284 views

How to estimate the phenotypic variation explained by top SNPs from a GWAS study?

I have conducted a large-scale GWAS study and got a few significantly associated SNPs. I used GEMMA with -lmm 1 options to run ...
5 votes
0 answers
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Parse RNA variant effect annotations ("r." format)

I've got annotations for splicing variants in a format like this (this is one variant): Variant: NM_004092.3:c.88+5G>A Effect: Retention; r.87_88ins1_88+10:p.(Ala31Glufs*23) I want to extract ...
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2 votes
2 answers
310 views

Produce .vcf file of ALL mutations in .bam file

I got tasked with a problem, that i thought would be quite simple to solve, but turned out to be quite tricky. Our lab is running targeted mutagenesis experiments in yeast using crispr base editors. ...
1 vote
1 answer
61 views

BWA: Detecting Variation between Reference Genome and Short-Read Sequences

I need to identify all loci in the short-read sequence at which the number of microsatellite repeats (i.e. number of copies of "AA," "GTC," etc.) differ from the reference genome, ...
2 votes
2 answers
2k views

Find rsIDs for GRCh37 SNPs and rsIDs for GRCh38 SNPs and compare for overlap

I have a long list of variant IDs that I generated as a result of research done one GRCh37 genomes (e.g. 13_28025615_G_C_b37). I want to get their rsIDs and compare ...
2 votes
1 answer
347 views

How to use -csvStats option?

I'm trying to get CSV files from snpEff -csvStats option and got stuck. I tried the code below and only got the vcf file with no contents. How can I use -csvStats option properly? ...
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3 votes
3 answers
4k views

Find overlap between VCF files

I have two VCF files and I want to compare the missing rate in each of them, but I want to only look at sites that are present in both files. How could I go about getting a list of positions that are ...
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1 answer
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Remove variants that do not map to human genome

[This question was also asked on Biostars] I received an hg38 VCF file that's had variants imputed with 1000 genomes. I've encountered some issues with the VCF; REF alleles that do not align to a ...
3 votes
1 answer
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Database for germline copy number variations in cancer

I am interested in looking at germline copy number variations in individuals that are at high risk of developing cancer. Are there any databases where I can look, if a CNV seen in our test case has ...
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Index VCF file for rapid access by rsID?

With tabix one can index a VCF file for rapid variant retrieval based on genomic position. I'm wondering if there are any tools that will index a VCF file to allow rapid retrieval using rsIDs and/or ...
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2 answers
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Evidence of emergence of "genuine" novel protein interactions by aa mutation [closed]

Anyone knows of an example of a protein that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other ...
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How to compute LD for pairs of variants with Plink

I have a set of SNPs (single nucleotide polymorphisms) { S1, S2, ..., SN } from approximately 200 humans. I wish to determine the linkage disequilibrium (LD) for a defined subset of these SNPs. By ...
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2 votes
1 answer
40 views

How to interpret amino acid representation

What is the difference between C383S and C383A? For C383S, does it mean Cysteine(C) position 383 in the sequence and its next amino acid connect to it is Serine(S)?
5 votes
2 answers
2k views

How can I remove (non-trivial) duplicates from a VCF file?

This is related to the question I asked here. Consider a vcf file that contains duplicate variants, but where the duplicates aren't simply the same thing in the same notation but instead one is a ...
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4 votes
1 answer
499 views

Are duplicate variants against the VCF standard?

I have been trying to understand an error that the EBI's vcf_validator gives when run on my vcf file. Consider this minimal file: ...
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3 votes
2 answers
272 views

Selecting 65000 SNPs where AF is close to 0.5 in all or most populations

I am evaluating the tool somalier (https://github.com/brentp/somalier) and I need to create a list of about 65,000 SNPs where the allele frequency (AF) is as close to 0.5 as possible across the most ...
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3 votes
1 answer
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Output from vcftools missingness

I'm new to data filtering on vcf data and vcftools. I performed variant calling on my dataset, CHR22, homo sapiens. I'd like to remove sites that are missing in more than 5% of individuals. ...
6 votes
1 answer
6k views

SNP vs Point Mutation

What is the difference between a Single Nucleotide Polymorphism (SNP) and a point mutation? I am quite confused in understanding these term as both of them refer to one base difference from the ...
3 votes
1 answer
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multiple COSMIC id for the same mutation

I would like to know why there are different entries for the same mutation in COSMIC, for example COSM6954941 and COSM12833 both refer to ERBB4 c.908C>A. In this specific case the field Gene name in ...
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1 answer
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How to paste RSIDs in CADD output

I want to paste RSIDs in CADD output as CADD does not give RSID column in its output. For this purpose I am using bedtools intersect to compare two files and have RSID column in my CADD file. This is ...
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2 votes
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Mutation detection using Varscan2 on RNA sequencing for estimating tumour clones with pyclone or other package

I would like to analyze my RNAseq profiles from bulk tissue samples (Paired-End, 50M reads/sample, tumour-normal pairs) with varscan2 to detect mutations. Then I ...
5 votes
1 answer
773 views

Simplest way to work out structural variant type?

In VCF 4.2, a structural variant (SV) can be described with the BND keyword in SVTYPE. For example, the following example is an ...
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4 votes
2 answers
397 views

Protein sequence from patient data

Currently, I am working on NGS data and my aim is to get significance prediction of variants present in the vcf file. As we know about SIFT Score for significance score prediction, I am trying to ...
4 votes
2 answers
810 views

GATK CombineVariants complains the contig order in the VCF files

I have called variants on two strains of C. elegans separately. I now want to merge the VCF files into one using the following code: Create a sequence dictionary of the reference sequence Sort the ...
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7 votes
1 answer
2k views

Merge 2 VCFs from different variant callers

I am working with WES data for detection of somatic variants and I have used two variant callers because no variant caller is complete in itself. I have used GATK Haplotypecaller for small variants ...
9 votes
2 answers
10k views

Converting a BAM file into VCF

I have NGS illumina RNA-seq reads from M. musculus (mm10). I am trying to find variants along the strand portion of the reads in the refseq (mm10). I mapped a pair of sequence files and generated a ...
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1 answer
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How to get unique somatic mutations for each individual patients

I have exome data 32 patients. My aim is to identify unique somatic mutations in each patients. For this I have completed my pipeline for Whole Exome Data analysis using various tools like BWA mem, ...
2 votes
1 answer
489 views

Can I export the SNPs between whole genome alignments using the command line?

I am using Mauve to align two whole genomes. I use the following command to get the alignment in xmfa format: ...
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1 vote
1 answer
199 views

Write the output of the VariantAnnotation package to file

I'm having some problems in exporting the annotations of some variants from a VCF file, after using the "VariantAnnotation" package from bioconductor. Below the script I've used: ...
2 votes
1 answer
42 views

remaining human genome variation that hasn't been sequenced?

Given all the genome variation information we have accumulated from resequencing human genomes up until now (early 2018), how much variation is left that hasn't been sequenced? EDIT: given one of the ...
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6 votes
1 answer
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How to represent a deletion at position 1 in a VCF file?

I am writing a small script to write a VCF file from short multiple sequence alignments, and stumbled into an interesting corner case. This is the way a deletion should be represented in VCF format (...
8 votes
4 answers
1k views

How to manipulate a reference FASTA or bam to include variants from a VCF?

I have some software which takes fastas as the input. I need to include SNVs and InDels from a VCF into the reference hg38 and then use this. The problem is, I don't know of an algorithmically sound ...
14 votes
7 answers
3k views

Is there public RESTful api for Gnomad?

I currently find Harvard's RESTful API for ExAC extremely useful and I was hoping that a similar resource is available for Gnomad? Does anyone know of a public access API for Gnomad or possibly any ...
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7 votes
1 answer
140 views

What is a good pipeline for using public domain exomes as controls?

I'm currently attempting association analysis with an extremely small set of patient exomes (n=10), with no control or parental exomes available. Downloading the ExAC VCF of variant sites (http://exac....
3 votes
2 answers
151 views

How can I find mutations associated with disease in human histone residues?

I would like to look if there are mutations in residues of human histones associated with any disease. For instance, if a mutation in residue K6 (lysine 6) of histone H2A1A is associated with any ...
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6 votes
2 answers
404 views

What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?

My understanding is that indels are from 1bp to 10Kb, and a healthy genome has ~400K-500K Indels. Surely most of these are small. What is the distribution of insertion sizes in a healthy human ...
13 votes
2 answers
344 views

Remapping genomic coordinates to account for indels

I'm interested in obtaining coding sequences of my favourite gene in all individuals from the 1000Genomes (and similar projects). I use GATK to get the right subset of variants, vcf-consensus to map ...
13 votes
2 answers
2k views

How to read structural variant VCF?

The IGSR has a sample for encoding structural variants in the VCF 4.0 format. An example from the site (the first record): ...
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19 votes
1 answer
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The state, limitations and comparisons of large variant stores

Background: We're increasingly needing some way of storing lots of variant data associated with lots of subjects: think clinical trials and hospital patients, looking for disease-causing or relevant ...
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13 votes
3 answers
354 views

Given a VCF of a human genome, how do I assess the quality against known SNVs?

I'm looking for tools to check the quality of a VCF I have of a human genome. I would like to check the VCF against publicly known variants across other human genomes, e.g. how many SNPs are already ...