BCFtools可用于处理VCF和BCF文件；具体可参考BCFtools说明文档进行详细学习。

This manual page was last updated 2022-02-21 and refers to bcftools git version 1.15.

键入bcftools可查看所有参数

• annotate .. edit VCF files, add or remove annotations

## 添加ID; 将染色体，pos，REF，ALT添加到ID
bcftools annotate --set-id +'%CHROM\_%POS\_%REF\_%FIRST_ALT' file.vcf

• call .. SNP/indel calling (former "view")

• cnv .. Copy Number Variation caller

• concat .. concatenate VCF/BCF files from the same set of samples

将不同染色体的VCF文件进行合并

• consensus .. create consensus sequence by applying VCF variants

• convert .. convert VCF/BCF to other formats and back

• csq .. haplotype aware consequence caller

• filter .. filter VCF/BCF files using fixed thresholds

• gtcheck .. check sample concordance, detect sample swaps and contamination

• head .. view VCF/BCF file headers

• index .. index VCF/BCF

• isec .. intersections of VCF/BCF files

• merge .. merge VCF/BCF files files from non-overlapping sample sets

• mpileup .. multi-way pileup producing genotype likelihoods

• norm .. normalize indels

对vcf中的InDel进行对齐

## 检查SV是否和ref一一对应
bcftools norm --check-ref e --fasta-ref Sp_YY_v2.fa $inputVCF

• plugin .. run user-defined plugin

• polysomy .. detect contaminations and whole-chromosome aberrations

• query .. transform VCF/BCF into user-defined formats

## 调取染色体和POS信息。
bcftools query -f '%CHROM\t%POS\n' output.vcf.gz
## 调取基因型是ALT的样本; 如果不在header里面，则用[]
bcftools query -f '%CHROM:%POS [%SAMPLE %GT]\n' -i'GT="alt"' file.bcf
## 调取VCF文件样本名称
bcftools query -l *vcf.gz >samples_list.txt

• reheader .. modify VCF/BCF header, change sample names

bcftools reheader -s test_changed_id  -o test.newid.vcf.gz test.vcf.gz
# -s 后面接需要替换的样本名称；共两列，第一列尾old name；第二列对应new name

• roh .. identify runs of homo/auto-zygosity

• sort .. sort VCF/BCF files

• stats .. produce VCF/BCF stats (former vcfcheck)

• view .. subset, filter and convert VCF and BCF files

（1）可从VCF中提取指定样本信息
bcftools index *vcf.gz
bcftools view -S samples *vcf.gz -Oz -o  *_sampels.vcf.gz
（2）对vcf进行过滤
bcftools view -i 'F_MISSING < 15 & MAC > 3'  -m2 -M2 *vcf -Oz -o  
*fil.vcf
(3) 指定染色体位置# 格式Chr\tpos
bcftools view -R Chr_pos *vcf.gz -Oz -o  *Chr_pos.vcf.gz
(4) 指定位点
bcftools view -T selected_snps.txt output.vcf.gz -o selected_snps.vcf.gz

• intersect

bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>

可用于检测两个gff文件中，是否存在🈚️overlap基因，使用-v参数
-v :Only report those entries in A that have _no overlaps_ with B.
        - Similar to "grep -v" (an homage).