I am trying to genotype NGS data from bam files using samtools and bcftools. I have a list of target SNPs in human hg19 for which I want the genotype. When I run bcftools view, I receive the error “cannot find ‘invert_targets_file’ while searching for ‘section.targets.invert_targets_file.’” When I run bcftools call, I receive the error message “cannot find ‘tgts_sec.’” Can someone help me overcome this problem? If someone could direct me to a pipeline for going from bam to targeted genotype I would be most appreciative.
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