search

sherman5 / RVS

Computes estimates of the probability of related individuals sharing a rare variant.
1 stars 1 forks source link

How to sequence affected members in a pedigree? #9

Open kmasroor opened 2 years ago

kmasroor commented 2 years ago

Hi, I'm trying to use the RVS code and am having difficulty with learning how to enter in the relevant sequencing data for the affected members of the pedigree. What would be the code for such a function?

abureau commented 2 years ago

Hi. Have you read the vignette at http://bioconductor.org/packages/devel/bioc/vignettes/RVS/inst/doc/RVS.html ? If your data is in Plink ped format, there is an example how to read it under 3.3 P-Value for Multiple Families, Multiple Variants. If your data is in vcf format, there is an example how to read it under 5.2 Example of Analysis of the Rare Variants in the Genomic Sequence of a Gene. Sections 3.3 and 5.2 also describe the most common analyses. If you have specific questions regarding either of these feel free to ask.

kmasroor commented 2 years ago

Thanks for getting back to me- I'm quite new to genome analyses, and therefore, I'm not totally comfortable with how to make either Plink ped or vcf format. I'm using a Macbook air. Which option is easier to do, and which would you recommend? Is there a specific program I need to download in order to save files as these types?

abureau commented 2 years ago

The end result of genomic sequence processing including variant calling will be vcf or Plink ped files, or a binary version of them. If you have raw sequencing data (e.g. fastq files) or partially processed data, this is not the place to learn about genomic sequence processing, as it is not the specialty of any of the authors of RVS. The Broad Institute is one resource https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows and there are others.