Manipulating VCF files

Create a VCF (​variant call format) file [with about any program that identifies variants], such as

• samtools' mpileup+bcftools:

  # One file of mapped reads
  samtools mpileup -uf indexed_genome My_mapped_reads.bam | bcftools view -bvcg - >| My_mapped_reads.raw.bcf
  # Multiple files of mapped reads
  samtools mpileup -uf indexed_genome *.bam | bcftools view -bvcg - >| Multiple_samples.raw.bcf
  

Convert from BCF (binary version of VCF) to VCF:

bcftools view My_mapped_reads.raw.bcf > My_mapped_reads.raw.vcf

Convert from VCF to BCF:

bcftools view -bS -D chr_list.txt My_mapped_reads.raw.vcf > My_mapped_reads.raw.bcf

Merge multiple VCF files -- works on raw VCF files but apparently not with those processed by vcf-annotate

# For each VCF file:
bgzip Variants_sample_A.raw.vcf
tabix -p vcf Variants_sample_A.raw.vcf.gz

Merge multiple bgzipped, tabixed files:

vcf-merge *.raw.vcf.gz >| Variants_all_samples.raw.vcf

Annotate a VCF file using ​vcf-annotate

# Apply all filters with default values:
vcf-annotate -f + Variants_all_samples.raw.vcf > Variants_all_samples.withTags.vcf
# Apply all filters with default values except for specified ones (MinAB(a) = 10; MinDP(b) = 20):
vcf-annotate -f +/a=10/d=20 Variants_all_samples.raw.vcf > Variants_all_samples.withTags.vcf
# Add custom filter(s) as described in file "My_filters.txt":
vcf-annotate -f My_filters.txt Variants_all_samples.raw.vcf > Variants_all_samples.withTags.vcf

For the last command, My_filters.txt contains a filter (such as an example one that calculates PLdiff values for 1/1 - 0/0 and 1/1 - 0/1, making sure that each difference is greater than 20). In this case, the filter is designed for selection, rather than filtering out.
For more examples, go to ​vcf-annotate and click on "Read even more".

{
    tag      => 'FORMAT/PL',
    name     => 'GoodPLdiff',
    desc     => 'Homozygote alternate and PLdiff greater than 20',
    apply_to => 'all',
    test     => sub {
            for my $pl (@$MATCH)
            {
                my @pls = split(/,/,$pl);
                if ( ($pls[2]-$pls[0])>20 && ($pls[1]-$pls[0])>20 ) { return $FAIL; }
            }
        return $PASS;
    },
},

Annotate variants with SNP IDs (if they overlap known SNPs)

# Index VCF file of SNPs (or other annotations)
bgzip dbSNP.version.vcf
tabix -p vcf dbSNP.version.vcf.gz
# Use annotation file to add info to ID column (if there's overlap between variant and annotation)
vcf-annotate -a dbSNP.version.vcf.gz -c CHROM,POS,ID,-,-,-,-,- -d key=INFO,ID=RS_ID,Number=1,Type=Integer,Description="SNPs from a subset of dbSNP" < My_variants.hg38.vcf > My_variants.hg38.dbSNP.vcf

See ​tabix for how to index BED or other file types. See ​vcf-annotate for details of last command.

Sort by chromosome and then coordinates

vcf-sort Variants.vcf > Variants.sorted.vcf

Validate VCF file (for use with GATK, for example)

java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T ValidateVariants -R /path/to/indexed/genome --variant:VCF SNPs.vcf

Convert from VCF to bed (using the ​BEDOPS toolkit):

vcf2bed < my_variants.vcf > my_variants.bed