[Genetics] Software to Phase for haplotype
I want to do haplotype phase? any software suggestion? 2000 genetic loci (1500 SNPs and 500 CNVs) in 2000 individual were included in the dataset. Thanks.
phase
• 2,665 views
•
link
updated
by
Ram
4.5K
• |
written
by
Shicheng Guo
963
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How can i exclude genetic variability inherited from parents in offspring ?
written by qstefano 2Hello everyone, I would like to exclude SNPs inherited from parents given offspring, in particular, i have VCF files generated with Haplotype caller for Father, …
-
Imputing missing genetic map distances from a bim file
written by devenvyas 77I 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 …
-
gnomAD and Bravo to download loss-of-function annotation
written by Shicheng Guo 963Hi 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 …
-
Multiple Haplotype Phasing Solutions in Plink
written by Shicheng Guo 963Plink 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? …
-
Fast way to extract part of genotypes data from 1000 Genome VCF files
written by Shicheng Guo 963Hi All, I need to do some permutation test to random sampling millions of SNPs set genotyping data from 1000 genome phase III dataset. each …
-
Forum: Genetic linkage analysis software tools and comparison
written by Shicheng Guo 963Here, 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 to find the haplotype info in population genomic databases
written by CrazyB 28How do I find the haplotype info from `ExAC` or `1000 Genomes`? `1000 genomes` states that their data released from phase 3 are all phased. …
-
Linkage Disequilibrium to Rare SNPs
written by Shicheng Guo 963Hi 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 …
-
What if I break my VCF file into small VCF files and then generate Haplotype indivually and merge i…
written by Being Bioinformatician 27have VCf file which contain 1500 SNPs. Due to computational limitation , it is not possible for generating Haplotypes using PHASE program. What if I …
-
GWAS or QTL with full factorial mating
written by Mashoon 0<p>Hi all,</p> <p>I made a full factorial mating of 58 males with 9 females to produce 2000 fish (some are full-sib, and some half-sib). 1500 …
Did you try samtools phase?