bcftools Tutorial on how to Count the number of variants per chromosome in a VCF file

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#Bioinformatics #DataScience #Linux #variants

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Download the example data here
bcftools manual page
1000 genome project ftp site
Install bcftools using anaconda
Install bcftools by building from source:

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00:00 intro and pc requirement
00:54 download the example data
04:24 index the VCF file
04:58 get the list of chromosomes
08:35 save the chromosome list to an output file.
09:35 count the variants per chromosome
10:20 include chromosomes to count
14:50 exclude chromosomes
17:40 automate the counting process
17:58 create a bash script to count all variants per chromosome

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Great work sir. Thanks for sharing your knowledge and expertise. In the course of coding along with you, my environment autocompleted a code line and upon running it I got the same result running the script "variant_counts.sh"

The code run in terminal is $ bcftools query -f '%CHROM\n' all.snps_indels.vcf.gz | sort | uniq - c

It looks much straightforward. I did learn a lot from using bash script to run codes watching this video though. Thanks a million sir.

emekapatrickchukwuka

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