Less stringent way of calling variants in PacBio data

Question

[TheCatalyst]

When I look at the 10X single cell PacBio mapped.bam file in IGV with allele frequency of >7% I see my SNPs of interest. However, when using bcftools call I don't see my SNPs of interest. Is there a way of calling the variants with bcftools that is less stringent?

Answer 1

[dthorbur]

There are many reason BCFtools may not have called that variant. Checking the quality, coverage, and other variants in that position is a good place to start. If the variant has poor PHRED scores, it's likely not real, for example.