Less stringent way of calling variants in PacBio data

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?

bcftools snps variant pacbio 10x

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updated 1.9 years ago by dthorbur

• written 1.9 years ago by TheCatalyst •

1 answer

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.

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written 1.9 years ago by dthorbur

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