1
result
•
updated 4.5 years ago
by
Istvan Albert
This recipe demonstrates a bacterial variant caller with minimap2 and bcftools
This recipe contains the code presented by Torsten Seemann in the blog post titled A Unix one-liner to call bacterial variants
The code from the above website has been generalized a bit with additional utility.
This recipe provides code that:
minimap2
to align the sequences and create a SAM outputbcftools mpileup
to generate the genotype likelihoods of each basebcftools call
to filter for multiallelic variants onlybcftools norm
to normalize each variant to a standard formbcftools filter
to remove variants with low quality (QUAL) or low coverage (DP)