I have an input set of variants in VCF format (
input.vcf.gz), which includes indels and SNPs. Multi-allelic variants are split across multiple lines. Using
bcftools view input.vcf.gz | vcf2bed | bedtools merge I then created a bed file
I would like to call only this predetermined list of variants using
bcftools (or other tools). How would I go about doing this?
I suppose I could specify the
targets.bed file as a parameter to
bcftools mpileup -R targets.bed --fasta-ref human_g1k_v37_decoy.fasta input.bam
... but that would still not allow me to specifically call the given list of variants in
input.vcf.gz. Any suggestions what I could do here?