image.png
https://github.com/vcftools/vcftools/releases
for name in `ls *.gz |awk -F "." '{print $1"."$2}' ` ; do
echo $name
vcftools --gzvcf ${name}.vcf.gz --remove-indels --recode --recode-INFO-all --out ${name}.snp.vcf
vcftools --gzvcf ${name}.vcf.gz --keep-only-indels --recode --recode-INFO-all --out ${name}.indels.vcf
done
如果是bcftools 产生的，建议用
bcftools view -v snps bcftools_filter.vcf >bcftools_snp_filter.vcf
bcftools view -v indel bcftools_filter.vcf >bcftools_indel_filter.vcf
参考：
Samtools+bcftools Call SNP
Question: Split Vcf File Into Snps And Indels
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