3
votes
Accepted
How to get a GISAID account? I registered months ago, still no reply!
I've got a GISAID account and it's subject to an approval process. It was pretty simple and is awarded quickly. There are definitely no fees needed. I personally didn't see the advantages over NCBI's ...
M__♦
- 11.9k
3
votes
Find common SNPs in multiple VCF files
A potential solution is to compress and index the files using bgzip and tabix, then use bcftools isec to find SNPs common to all three files, e.g.
...
- 695
3
votes
Accepted
How to represent random sequence elements in SBOL?
This sounds like a job for the CombinatorialDerivation class, which is designed for representing libraries and the relationship between derived designs and the ...
- 653
3
votes
pathogeniticy prediction tool
Venus
I am the developer of venus.cmd.ox.ac.uk, which is a site that given a mutation makes the variant (and gives the ∆∆G) and shows what residues are nearby and whether these appear in clinVar or ...
- 4,234
3
votes
Accepted
Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)
A comment from a Nextclade's user satisfies my actual needs, I will post it here for future reference:
Hi - one possible source is the metadata file for UCSC’s daily-updated tree of public SARS-CoV-2 ...
- 2,676
2
votes
Inheritance annotation for nsSNPs
If you only have a small number of genes, OMIM is a very easy way to do this.
For example:
If you have too many to do manually, I suspect there is an easy way to query lists, although I'm not sure ...
- 1,679
2
votes
Produce .vcf file of ALL mutations in .bam file
You could perform an mpileup with samtools. I think this would be the most sensitive approach. Here's the man page: http://www.htslib.org/doc/samtools-mpileup.html
You might want to disable BAQ ...
- 2,236
2
votes
Produce .vcf file of ALL mutations in .bam file
Ensure that the variant caller stringency is relaxed all the way. For example in freebayes use ...
- 839
2
votes
Accepted
How to compact variant data to their genes without bias?
Its very easy, just let the ML sort this out for you and that is its advantage, You're thinking of GLM style calculation where you pre-screen the data with bivariate plots, where there needs to be ...
M__♦
- 11.9k
2
votes
SNPEFF genome build with specific codon usage
codon table issue
I solved the issue with codon tables, the correct way to specify a table is the following:
...
- 141
2
votes
Q: What analyses can I perform with a completely phased genome assembly?
Some population genetic inference methods require the data to be phased because they look for long stretches of matching alleles between individuals, rather than just matching genotypes. Here, '...
- 1,679
2
votes
Accepted
1
vote
Standardizing Variant IDs best practise
Thoughts on the described method from Bristol?
I don't immediately see the benefit to this over rsIDs.
What might be the maximum length for an indel we could encounter?
Potentially very long. ...
- 513
1
vote
genotyping or variant calling in R
Samtools/bcftools/tabix is available in R via Rsamtools.
SEQprocess also provides wrappers for different tools such as GATK and bowtie.
More utility packages are noted here.
- 3,804
1
vote
Compare VCF files
If I understood you correctly you are searching for a way to represent the genomic locations in your vcf file. However, the vcf file is already a human readable file (vcf specification).
The first ...
- 11
1
vote
Accepted
Name this alternative INDEL format
The alternative deletion representation that you are describing, i.e. using . to represent alternate alleles that are not present, is allowed within the definition ...
- 13.8k
1
vote
Accepted
syndip dataset for benchmark variant
If you want the truth VCF, it is full.37m.vcf. rep2.37.broad.hc.raw.vcf.gz is an example call set by GATK.
- 6,485
1
vote
Dictionary and index of vcf for base recalibration step
I have also encountered this error before in cases where there was something wrong with the VCF file I was supplying.
Double check your command to ensure that you are feeding it the file you believed ...
1
vote
Counting the co-occurrence of variants A and B in an aligned sequencing read
Related question: Access base aligned to particular reference position
After an initial effort posted here, I ended up rewriting this and testing it a little, and posted the script here. It still has ...
- 3,804
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