For example: bcftools filter -O z -o -i QUAL>50 in.vcf.gz bcftools view -O z -o -e QUAL<50 in.vcf.gz The quality field is the most obvious filtering method. fasta, masking sites from the list fileīcftools consensus -mask $1_lowDP_trueSNPs.list -fasta-ref $REF $1.Q30_ > $1.consensus. Bcftools can filter-in or filter-out using options -i and -e respectively on the bcftools view or bcftools filter commands. We can also filter based on these proportions. For example, 0.75 means that samples with greater than 75 missing data are filtered away. One-liner to calculate proportion missing data per sample in VCF/BCF file.

Simply replace <, <, and < with the input file name, output file name, and proportion missing data at which points samples begin to get excluded, repectively.

# Zip and index the vcf file of true SNPs to save space We can also filter based on these proportions. But Bcftools will interrupt with Comparison between samples is not supported, sorry. REF= 'GCF_002837175.2_ASM283717v2_genomic_headers_fixed.fa 'Ĭp $vcf_dir/ $1.Q30_ * $ ' > $1_trueSNPs.listĬat $1_lowDP.list $1_trueSNPs.list | sort -k1,1 -k2,2n -u > $1_lowDP_trueSNPs.list So, we can use bcftools view -i GT 0GT 1 trio.vcf to select subvcf that genotype of sample1 and sample2 is identical. The columns ID, QUAL, FILTER, INFO and FORMAT can be edited, where INFO tags can be written both as INFO/TAG or simply TAG, and FORMAT tags can be written as FORMAT/TAG or FMT/TAG.

Module load bioinfo-tools samtools/1.10 bcftools/1.10 tabix/0.2.6 vcftools/0.1.16 htslib/1.3 bcftools isec -n +2 bgzip -c > Alternatively, if you wanted just statistics on the numbers of SNPs/variants or genotypes in common between files, you could use the vcf-compare tool that comes with vcftools. If the annotation file is a VCF/BCF, only the edited columns/tags must be present and their order does not matter.

Bcftools filter vcf