Platypus and IBD sharing
I was wondering if anyone here has worked with Platypus and possibly know if the software is able to detect IBD sharing among individuals?
sequencing
next-gen
genome
• 1,631 views
•
link
written
by
reza.jabal
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Are truseq adapter sequences picked up by FASTQC?
written by bioinfo •Hello, I am testing a new software that is supposed to automatically detect adapters and remove them. I am using the adapters shown here: https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/TruSeq/UDIndexes.htm …
-
Germline2 IBD
written by Alexandra •Hi all! I've performed an IBD analysis by Germline2 software, resulting in OUT.match file. Now, I want to plot this results but I don't know …
-
Recs for what to use for analyzing IBS sharing (from phased, imputed VCFs)?
written by devenvyasI have imputed GZ.VCFs from Beagle 4.0 based on some ancient DNA VCFs (24 individuals). Beagle phased the genotypes in their output. I am looking …
-
Issue with ExAC and 1000g hg38 lifted-over data and systematic failure of annotation softwares!
written by reza.jabal**ExAC** data with `hg38 coordinates` has been around for filter-based annotation since late 2015, but it seems there is a systematic problem with the use …
-
VerifyBamID freemix score?
written by reza.jabalI was wondering if anyone here can explain how does the freemix score is calculated and what it is exactly! I have read the paper …
-
How accurate is the IBD calculation by plink?
written by MAPKI was trying to calculate the IBD values for about 100 individuals all likely to be unrelated. I tried to use plink tool ( http://pngu.mgh.harvard.edu/~purcell/plink/ibdibs.shtml …
-
Identifying Split-Reads in WES data!
written by reza.jabalHello everybody; Here I've got a patient with an unidentified neurodevelopmental complication and primary WES analysis with candidate gene approach resulted in no significant finding. …
-
IBD vs IBS
written by MAPKI was reading these two papers, (http://www.nature.com/nrg/journal/v11/n11/full/nrg2865.html and http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025522/) where I got confused with the way they have discussed IBD and IBS and the way …
-
VCF to ANNOVAR format
written by reza.jabal<p>Here, I've got a VCF file I want to convert to ANNOVAR format through running the following command, but apparently it is not working!</p> <pre> …
-
Calculating Ibd Using R Package
written by Hypotheses •<p>Hi all,</p> <p>Does anyone know whether there is any R package or function to calculate IBD (identity by descent) sharing? I have been trying to …