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Most people do not understand the knowledge points of this article "how to use bedtools to calculate the number of mutations in different regions of each chromosome in VCF files", so the editor summarizes the following contents for you. The content is detailed, the steps are clear, and it has a certain reference value. I hope you can get something after reading this article. Let's take a look at this article entitled "how to use bedtools to count the number of mutations in different regions of each chromosome in a VCF file".

1. Obtain the length information of each chromosome of the genome

$samtools faidx genome.fa# generates the first column of chromosomes in the gemome.fa.fai file The second list corresponds to the chromosome length chr01 44488843 7 44488843 44488844chr02 38522657 44488858 38522657 38522658chr03 34302425 83011523 34302425 34302426chr04 31904921 117313956 31904921 31904922chr05 31465669 149218885 31465669 31465670chr06 29481096 180684562 29484896 29481097chr07 26142479 210165666 26142479 26142480chr08 23295356 236308153 295356 23295357chr09 21309744 259603517 21309744 21309745chr10 20413421 280913269 20413421 20413422

two。 The region file is produced according to the length of the chromosome:

$bedtools makewindows-g genome.fa.fai-w 100000 > region.bed$ head region.bedchr01 0 100000chr01 100000 200000chr01 200000 300000chr01 300000 400000chr01 400000 500000

3. Input vcf file to count the number of variations in different regions

The above $bedtools coverage-a region.bed-b q4.vcf-counts > result.txt is about "how to use bedtools to calculate the number of mutations in different regions of each chromosome in VCF documents". I believe we all have a certain understanding. I hope the content shared by the editor will be helpful to you. If you want to know more about the relevant knowledge, please follow the industry information channel.

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