Compare 4 vcf files with vcftools
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6.3 years ago

mmm I tried with vcftools and --diff to see which snps, indels... share 4 individuals from a family. But with this code seems just compare two individuals

vcftools --vcf 2.vcf --diff  2.vcf --diff 3.vcf --diff 4.vcf --out compareall.xls

so at end I did like someone posted in this forum

cat 2.vcf 4.vcf 10.vcf > 2410.vcf

vcftools --vcf 2410.vcf --recode --recode-INFO-all --diff padre.vcf --out compareall.xls

I do right?

Isn't another way to do like on first stage?

Thanks :)

vcf • 3.8k views
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see if this tool will work.

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well...I dont know but always I get some trouble to insatll Python packages

I do like say

pip install https://github.com/Clinical-Genomics/taboo/zipball/master

I sort my samples, but when I run this code in terminal where I have my files

taboo compare sample*.sorted.vcf > results.txt

says taboo command not found ;_;

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well no idea how...but I managed to install taboo

now i get this

taboo compare sample2.sorted.vcf sample10.sorted.vcf > results.txt
taboo compare sample*.sorted.vcf > results.txt


both codes Aborted!
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