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 targets.bed
.
I would like to call only this predetermined list of variants using samtools
and/or 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
:
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?