# Useful commands
| $ vcftools --gzvcf input.vcf.gz --keep id.txt --recode --stdout | gzip -c > out.vcf.gz |
| $ vcftools --gzvcf input.vcf.gz --positions SNP_list.txt --out nucleotide_diversity |
| $ vcftools --gzvcf input.vcf.gz --chr 1 --from-bp a --to-bp b --recode --recode-INFO-all --out chr1_analysis |
| $ vcftools --gzvcf input.vcf.gz --freq --out freq_analysis |
| $ vcf-compare first.vcf.gz second.vcf.gz |
# Issues
⚠️ Error
| "Can't locate Vcf.pm in @INC" when using perl-vcf modules |
🔧 Solution
| $ export PERL5LIB=/path to vcftools/share/perl5 |
