Questions tagged [variation]

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

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17
votes
1answer
419 views

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 ...
8
votes
2answers
7k 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 ...
4
votes
1answer
355 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: ...
12
votes
2answers
274 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 ...
8
votes
4answers
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 ...
3
votes
2answers
147 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 ...