CoSA v7.3.0 update: Labcorp (1.2kb amplicon) protocol, variant calling, and VCFCons

[mag...@gmail.com]

Hi all,

The 1.2kb amplicon SARS-CoV-2 protocol used by Labcorp is at:

https://www.pacb.com/research-focus/microbiology/COVID-19-sequencing-tools-and-resources/

CoSA is now at v7.2.0. The wiki contains the most up-to-date info on how to analyze it starting from CCS BAM files.There are multiple choices for variant caller, as long as it gives you a VCF file.

https://github.com/Magdoll/CoSA

Use VCFCons.py to generate an appropriate filtered VCF +  consensus sequence fasta.

Please file bugs on GitHub Issues. 

-Liz