Questions tagged [haplotypes]
Genetic code involving inherited DNA present as a single copy, which for eukaroyotes is the mitochondrion and in bacteria is the complete genome.
5 questions with no upvoted or accepted answers
Weird data in VCF file
I am using GATK HaploTypeCaller for SNP calling. I have 300 samples. As far as I understand that if a sample is missing a SNP it should be denoted by ./., however, I am getting a lot of values like 0/...
How to calculate switch errors on plink formatted phased genotype data?
everyone! I'm working with haplotype inference algorithms in pedigree genotype data, and I would like to know if there is a tool or script to calculate switch errors on phased pedigree data (Plink ...
Why does gene count increase drastically after scaffolding with Hi-C data?
I have a conceptual question. I have a diploid, outcrossing plant genome assembly of ~1.1 Gb size. The original assembly is generated from PacBio reads. After genome annotation with the ...
How to format the Nexus file to create geographical maps with haplotypes in PopArt?
I'm trying to create a map in PopArt that allows me to visualise the distribution of several species. These are my Traits (=species) and GeoTags blocks: ...
How to plot a graph of Linkage disequilibrium with limited information
I have a snp information in an excel file and I used SNPstat to do some analysis. But I also need a plot of LD for these snps. But my file is not formatted as the most programs required (.ped, hapmap, ...