bcftools 工具功能集合

bcftools +counts ChrMT-Run9-TAUIND-raw-toDistribute.vcf.gz 
Number of samples: 6191 
Number of SNPs: 5739 
Number of INDELs: 930 
Number of MNPs: 0 
Number of others: 0 
Number of sites: 6242

转换vep vcf 注释 为 普通txt 格式
bcftools +split-vep -f '%CHROM\t%POS\t%REF\t%ALT\t%CSQ\n' -d -A tab input.vcf >> output.tsv


### 统计vcf 行数
bcftools index <file>
bcftools index --nrecords <file>

bcftools concat -O z -o 2.subset_as_gsaID_40sample_chrall.vcf.gz $(ls ./2.subset_as_gsaID_40sample_chr*.vcf.gz|sort -V)

### 合并染色体或者chunk
bcftools concat  input*.vcf.gz -O z -o output


### bcftools 去除多态性位点 并提取 sample
bcftools view -c 1 -S samples.txt total_chroms.vcf.gz -O z -o total_extract_minac.vcf.gz

### list sample and sort
bcftools query -l /disk/project/imputation/topmad_imputed/topmad_imputed.dose_delchr.vcf.gz|sort -V

for i in `seq 1 22`
do
echo "chr$i\t$i"
done > chr.list
### modify vcf chrom "chr"
bcftools annotate --rename-chrs chr.list -O z -o topmad_imputed.dose_delchr2.vcf.gz topmad_imputed.dose.vcf.gz

### bcftools 合并染色体 或者chunk

bcftools concat -O z -o topmad_imputed.dose.vcf.gz $(ls */*dose.vcf.gz|sort -V)