BCFTOOLS view | BCFTOOLS split | Split or Subset VCF files based on Sample IDs

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Download the example data here

Install bcftools using anaconda
Install bcftools by building from source:

Sections of this video

00:00 intro
01:04 download the example data
04:36 get the sample ids
05:49 get the sample ids and save to an output file
07:02 Subset vcfs
07:05 include samples to subset
20:04 exclude samples
31:02 split vcf files into individual samples
  1. Bioinformatics Coach
  2. bcftools split
  3. bcftools variant calling
  4. bcftools
  5. bcftools tutorial
  6. bcftools mpileup
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Комментарии
Автор

Regarding script writing as your are doing for Nextflow, I think you need to explain further. You need to mention for the beginner as well.

dr.abdullahkheshgi-biology
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I am not doing critic jusy giving a suggestion. Thanks for the great work and valuable effort. Stay blessed

dr.abdullahkheshgi-biology
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I have a trio file with x chromosome so how can I separate male and female samples from it

BioFreelanceServices
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I have a lot of catching on to do. I have been away doing a lot of wet lab

ifyifemanima
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Hi, I am trying to learn genomic and transcriptomic data analysis will a intel i5 12th gen sufficient for this or I will need a more powerful cpu?

rajneeshdadwal