= Manipulating VCF files = 

Create a VCF ([http://en.wikipedia.org/wiki/Variant_Call_Format 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 (applying all filters with default values):
{{{
cat Variants_all_samples.raw.vcf | vcf-annotate -f + > Variants_all_samples.withTags.vcf
}}}

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
}}}