bcftools其实很好用

*bcftools filter

*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)

bcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:

bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:

bcftools view -f PASS filename.vcf.gz

*printing variants withoud header:

bcftools view -H

*printing variants on a particular region:

bcftools view -r chr20:1-200000 -s NA20818,NA20819 filename.vcf.gz

*print all variants except for the ones falling within region:

bcftools view -t ^chr20:1-30000000 ex_bams.samtools.20161231.vcf.gz >out.vcf

*view the positions passed in a file (accepted files are .vcf and .bed):

bcftools view -R 0002.vcf in.vcf.gz

*view the positions passed in a tsv file:

bcftools view -R 0002.tsv in.vcf.gz

# The format of 0002.tsv:

20 79000 80000

20 90000 100000

*printing out only the chr info:

bcftools query -f '%CHROM\n' filename.vcf

/

*now, print out the chr\tpos

bcftools query -f '%CHROM\t%POS\n' filename.vcf

/

*now, print out the AF INFO field

bcftools query -f '%INFO/AF\n'

/

#getting a particular annotation from the VCF

bcftools query -f '%QUAL\n' 0002.vcf

/

#printing chr pos and a particular annotation from a VCF:

bcftools query -f '%CHROM\t%POS\t%INFO/DP\n' in.vcf.gz

/

#printing out the sets assigned by GATK CombineVariants

~/bin/bcftools-1.6/bcftools query -f '%set\n' out_combine.vcf.gz |sort |uniq

/

0#printing a list of samples from a VCF:

bcftools query -l test.vcf

/

#also, the FORMAT annotations can be obtained by:

~/bin/bcftools/bcftools query -f '[%GT]\n' ../0002.vcf |wc -l #the GT in this case

/

*selecting snps from file:

~/bin/bcftools/bcftools view -v snps lc_bams.bcftools.20170319.NA12878.vcf.gz

/

*selecting the variants from a VCF (excluding 0|0 genotypes)

bcftools view -c1 input.vcf

/

*selecting the non-variants from a VCF(AC=0)

bcftools view -H -C0 concat.allchrs.sites.vcf.gz

/

#filtering:

/

#using one of the INFO annotations (IDV)

bcftools filter -sFilterName -e'IDV<5' input.vcf

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#OR logical operator:

bcftools filter -sFilterName -e'DP>50000 | IDV<9' input.vcf

/

#filtering on FORMAT annotation:

bcftools filter -sFilterName -e'FORMAT/DP<5' input.vcf

/

#filtering on INFO annotation:

bcftools filter -sFilterName -e'INFO/DP<5' input.vcf

/

#printing out variants that pass the filter:

~/bin/bcftools/bcftools view -f.,PASS lc_bams.bcftools.20170411.exc.norm.SNP.filtered.vcf.gz

/

#bcftools stats and filtering:

~/bin/bcftools/bcftools stats -f "PASS,." file.vcf

/

#select only biallelic (excluding multiallelic) snps

bcftools view -m2 -M2 -v snps input.vcf.gz

/

#select only the multiallelic snps

bcftools view -m3 -v snps input.vcf.gz