Hello everyone, I would like to exclude SNPs inherited from parents given offspring, in particular, i have VCF files generated with Haplotype caller for Father, …

Dear All, Is there anything should be careful for the workflow developed for Genetic variation calling (SNPs) from bulk RNA-seq dataset. Is there mature established …

I have a Plink dataset with 7.1 millions biallelic SNPs (which are in 1000G phase 3). I was able to recover genetic map distances for …

Hi All, I want to download the annotation of 'loss-of-function' annotation in [gnomAD][1] and [Bravo][2] database. However, it seem you can find these annotation when …

Plink really does a great job when it calculate LD and even for multiple haplotypes/phasings, LDs are provided. However, the posterior probability were lost, right? …

Hi All, I need to do some permutation test to random sampling millions of SNPs set genotyping data from 1000 genome phase III dataset. each …

Here, we hope to talk about the comparison between different genetic linkage analysis software tools. Several years ago, I used ***Merlin*** to do linkage analysis …

How do I find the haplotype info from `ExAC` or `1000 Genomes`? `1000 genomes` states that their data released from phase 3 are all phased. …

Hi colleagues, Just very simple question. When we calculate LD, we need P(A),P(a),P(B),P(b) and then D=P(AB)-P(A)P(B) r=P(AB)-P(A)P(B)/sqrt(P(A)P(a)P(B)P(b)) However, for raw SNPs or mutation, P(A) or …

have VCf file which contain 1500 SNPs. Due to computational limitation , it is not possible for generating Haplotypes using PHASE program. What if I …