vcftools

习惯：Always使用bgzip生成vcf.gz文件

并用tabix生成index，使得vcftools和GATK中直接使用vcf.gz文件。

bgzip和tabix包含在samtools/htslib内。

samtools/htslib/bgzip -c file.vcf > file.vcf.gz
samtools/htslib/tabix -p vcf file.vcf.gz

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小模块
在vcftools/vcftools-build/bin/中的小程序，实现简单的特定功能。列出几个最常用的。其他更多

使用前需要导入perl_module lib

export PERL5LIB=/home/wanglizhong/software/vcftools/vcftools-build/lib/perl5/site_perl/5.8.8:$PERL5LIB;

单个vcf

重新计算INFO里的AN和AC

fill-an-ac
重新计算AN和AC 并加入INFO中。

zcat in.vcf.gz|fill-an-ac > out.vcf

vcf2fa

vcf转成一致性序列(consensus sequence)。

cat ref.fa|vcf-consensus file.vcf.gz > out.fa

# 其中某一个个体
cat ref.fa|vcf-consensus -s sampleA_ID file.vcf.gz > out.sampleA_ID.fa

# 只有某一个haplotype（1或者2）
cat ref.fa|vcf-consensus -H 1 file.vcf.gz > out.hap1.fa

取出部分个体

vcf-subset -c

vcf-subset -c NA0001,NA0002 file.vcf.gz | bgzip -c > out.vcf.gz

vcf里的信息自定义输出

vcf-query file.vcf.gz 1:10327-10330
vcf-query file.vcf -f '%CHROM:%POS %REF %ALT [ %DP]\n'

Usage: vcf-query [OPTIONS] file.vcf.gz
Options:
   -c, --columns <file|list>           List of comma-separated column names or one column name per line in a file.
   -f, --format <string>               The default is '%CHROM:%POS\t%REF[\t%SAMPLE=%GT]\n'
   -l, --list-columns                  List columns.
   -r, --region chr:from-to            Retrieve the region. (Runs tabix.)
       --use-old-method                Use old version of API, which is slow but more robust.
   -h, -?, --help                      This help message.
Expressions:
   %CHROM          The CHROM column (similarly also other columns)
   %GT             Translated genotype (e.g. C/A)
   %GTR            Raw genotype (e.g. 0/1)
   %INFO/TAG       Any tag in the INFO column
   %LINE           Prints the whole line
   %SAMPLE         Sample name
   []              The brackets loop over all samples
   %*<A><B>        All format fields printed as KEY<A>VALUE<B>
Examples:
   vcf-query file.vcf.gz 1:1000-2000 -c NA001,NA002,NA003
   vcf-query file.vcf.gz -r 1:1000-2000 -f '%CHROM:%POS\t%REF\t%ALT[\t%SAMPLE:%*=,]\n'
   vcf-query file.vcf.gz -f '[%GT\t]%LINE\n'
   vcf-query file.vcf.gz -f '[%GT\ ]%LINE\n'
   vcf-query file.vcf.gz -f '%CHROM\_%POS\t%INFO/DP\t%FILTER\n'

将个体顺序重排

Reorder columns

将file.vcf.gz按照template.vcf.gz顺序重排

vcf-shuffle-cols -t template.vcf.gz file.vcf.gz > out.vcf

vcf postions Reorder

vcf-sort file.vcf.gz > out.vcf
zcat file.vcf.gz| vcf-sort > out.vcf

转换成tab格式

zcat file.vcf.gz | vcf-to-tab > out.tab

输出如下：

#CHROM  POS REF 05537
chr2    131 T   T/T
chr2    437 G   G/G
chr2    453 G   G/G
chr2    469 G   G/G
chr2    526 G   G/G
chr2    618 G   G/G
chr2    745 A   A/A
chr2    756 T   T/T
chr2    760 T   T/T

计算tstv

cat file.vcf | vcf-tstv

vcf格式校验

vcf-validator file.vcf.gz

多个vcf

比较多个vcf里SNP位置的overlap

可以用结果画维恩图Venn-Diagram。

# run
vcf-compare test.vcf.gz test2.vcf.gz test3.vcf.gz|grep ^VN | cut -f 2-

# results
VN      94      test.vcf.gz (9.5%)      test2.vcf.gz (22.3%)    test3.vcf.gz (48.5%)
VN      100     test.vcf.gz (10.1%)     test3.vcf.gz (51.5%)
VN      327     test.vcf.gz (32.9%)     test2.vcf.gz (77.7%)
VN      473     test.vcf.gz (47.6%)

合并多个染色体chr/scaffold

1.个体（header）需完全相同。

vcf-concat chr1.vcf.gz chr2.vcf.gz | bgzip -c > all.vcf.gz

2.合并有不同个体的多个vcf

• 最好有相同Postions，缺失的默认会被填上miss（.）

  vcf-merge A.vcf.gz B.vcf.gz C.vcf.gz | bgzip -c > out.vcf.gz

• 把mis的用自定义genotype（0|0，0/0，1/1等等）填上

  vcf-merge -R '0|0' A.vcf.gz B.vcf.gz C.vcf.gz | bgzip -c > out.vcf.gz

• bcftools

  samtools/bcftools/bcftools merge --merge all --no-version --threads 10 file1.vcf.gz file2.vcf.gz |bgzip -c > merge.vcf.gz

3.一行命令合并vcf，巧用括号

# Merge (that is, concatenate) two VCF files into one, keeping the header
# from first one only.
(zcat A.vcf.gz | grep ^#; zcat A.vcf.gz | grep -v ^#; zcat B.vcf.gz | grep -v ^#; )| bgzip -c > out.vcf.gz

找vcf overlap/互补位置

# 输出两个vcf里共有的
vcf-isec -n +2 A.vcf.gz B.vcf.gz | bgzip -c > out.vcf.gz

# 输出第一个vcf里有，其他vcf（B和C及后面更多）里没有的
vcf-isec -c A.vcf.gz B.vcf.gz C.vcf.gz | bgzip -c > out.vcf.gz