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8 votes
Accepted

Is there any difference between SNPs 'AG' and 'GA' in association analyses?

Could you please show us the context in which this appears, as you seem to be interpreting this differently to Devon. If it's appearing as you say, GA and AG, then Devon is right, this usually means ...
8 votes
Accepted

How to get a list of genes corresponding to the list of SNPs (rs ids)?

I wonder if there is a simpler solution recently? (and hopefully, I can solve it within the scope of python. ) A simpler solution, I don't know... but this is at least one Python solution using ...
  • 366
7 votes

How to get a list of genes corresponding to the list of SNPs (rs ids)?

I can show you a simple way in R, using biomaRt. Let's say you have two snp ids you want to exmine. ...
  • 3,551
6 votes
Accepted

How to deal with correlated SNPs in GWAS?

What you are attempting to do is known as LD-pruning. As @Emily_Ensembl said, it is not customary to do this for standard association tests: it is possible that one of the SNPs you remove is causal, ...
  • 463
6 votes

What will be an appropriate mathematical distribution for SNP data?

Simulating genotypes with realistic correlation structures is indeed not so simple, and there's quite a few papers dedicated entirely to that (e.g. https://bmcgenet.biomedcentral.com/articles/10.1186/...
  • 463
6 votes
Accepted

Where can I find a list of SNP rs IDs that belong to the X chromosome?

You just searched for X[Chromosome], you didn't specify a species. Presumably, your dataset comes from a specific species, so you should limit your search to that ...
  • 8,235
6 votes
Accepted

SNP vs Point Mutation

The difference between the two depends on to whom you talk ;) You are right: both refer to one base difference from the sequence. Usually the term "mutation" is used if the change has an impact on ...
  • 1,332
6 votes

Variant calling without matched normal sample

If you just want to filter out calls present in dbSNP then use: ...
  • 19.3k
5 votes

Convert rs ID of one hg build to rs IDs of another build

You can assume that the overwhelming majority of rsIDs are the same between GRCh37 and GRCh38 (they're semi-stable IDs). There are, however, a number of rsIDs that are present only in GRCh37, which ...
  • 19.3k
5 votes

Identifying relevant SNPs from a list

What you are looking for is SNP annotation. If you have the chromosome:position reference and alternate alleles for your SNPs of interest, it can be as simple as uploading them to the variant effect ...
  • 393
5 votes
Accepted

PLINK clump behavior on missing SNPs?

Most likely, the GWASs that generated your summary statistics used other imputation panels than 1000G, like HRC. Clearly, PLINK can't estimate the LD for SNPs that aren't found in the reference, and ...
  • 463
5 votes
Accepted

SNP-phenotype association analysis only using the SNPs on a specific gene

I know that the GWAS association p-value threshold is 1e-8 This may be a common threshold of statistical significance that is used, but it's definitely not an absolute value. It's a hack to try to ...
  • 12k
5 votes
Accepted

Tool or script to parse annotated VCF files

(edit)you can filter the VCF annotations with snpsift, I've also written a VcfFilterSequenceOntology http://lindenb.github.io/jvarkit/VcfFilterSequenceOntology.html I've written vcf2table: http://...
  • 1,473
5 votes

remaining human genome variation that hasn't been sequenced?

In theory, almost any base in the human genome may mutate, so you have billions of variants to go. Ok, this is not so useful. A related and potentially useful question is: given a human, what is the ...
  • 6,023
5 votes

SNP located within a promoter region (pig)

As far as I'm aware, Illumina provide CSV annotation files for all their sequencing chips, which can be used when they can't be found in Bioconductor. You can find annotation information for the ...
  • 12k
5 votes
Accepted

Use of heterozygous SNPs in cancer research: why?

I’m no longer working in tumour sequencing so I’m by no means an expert. But in a nutshell, the reason is that, as indicated, homozygous SNPs aren’t informative: if your allelic fraction is 100%, ...
5 votes

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

Just use bcftools view for filtering: $ bcftools view -i 'AF>0.3 && AF<0.7' input.vcf.gz > output.vcf To truncate this list to 65,000 SNPs count ...
  • 1,332
4 votes

Is there a way to quickly verify the presence of some SNPs in Fastq files?

Try this pipeline: Clean raw fastq files (trimmomatic) Align clean fastq files to the reference genome (dna-to-dna aligner of your choice) Convert the alignment sam file to bam (samtools) Call SNPs ...
  • 2,656
4 votes

How does one construct a cladogram of intraspecies relationships?

Even with inbreeding and other genetic phenomena that might mask actual evolution of these cultivars, any phylogenetic methodology would be capable of determining relationships accurately. Try ...
  • 182
4 votes

Is there any difference between SNPs 'AG' and 'GA' in association analyses?

Is "user5054" the same as "user5504"? No? Exactly. Not only does order matter, it's incredibly vitally important. AG and GA are ...
  • 19.3k
4 votes

How to retrieve SNPs data of different humans?

If you mean that you want snps from individuals, instead of all together, you can find them in 1000 genomes. Here different individuals from different populations are sequenced and variants are called,...
  • 3,551
4 votes
Accepted

Using Beagle 4.1 for phasing and IBD - chromosomes

OK, I ended up contacting one of the authors of the program, who kindly answered to my question: Either approach should work, [i.e. running the analysis by chromosome vs joining the data together] ...
  • 201
4 votes

Does the ".full.aln" file produced by snippy-core contain all bases of my input sequences aligned to the reference genome?

snippy-core is a tool that processes the snippy_outdir_{1..n} folders and produces the following files: ...
4 votes
Accepted

What does PCA mean on GWAS

From my memory of what a statistician told me, a PCA aims to determine independent linear combinations of variables (i.e. genotypes) that account for the most variation in the dataset. With 10 million ...
  • 12k
4 votes
Accepted

How do I remove allele annotations from SNP Ids in .bim file?

The simplest approach is to remove the first occurrence of a _ followed by a capital letter, another _ and another capital ...
  • 8,235
3 votes

Show presence of known mutation in RNA-seq data

If you only have one gene and you only need to do this once then the simplest possible workflow is to generate the aliment using STAR (optimally with the two pass method) and open the two resultant <...
  • 1,029
3 votes

Show presence of known mutation in RNA-seq data

For counting reads I use mpileup, e.g. samtools mpileup --reference hg38.fa -r Chr10:18000-45500 input.bam, which will give base-resolution coverage for a BAM file. ...
  • 12k
3 votes

Identifying relevant SNPs from a list

ANNOVAR is another tool that will help you functionally annotate genetic variants. It will tell you if the variant is known in COSMIC or Clinvar databases, which AA change will occur, if it's a ...
3 votes

PLINK clump behavior on missing SNPs?

You can use imputation for guessing at what the missing SNPs might be based on known LD patterns in populations. This procedure will give you an idea of whether the recombinational history of genomic ...
  • 12k
3 votes
Accepted

Given a Genomic Ranges of SNPs, how to inject these SNPs in genome via BSGenome?

This seems relatively complicated given the structure of a BSGenome object. The creator of the package answered this question previously on the Bioconductor support forums: https://support....
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