CoSA v2.6.0 update: whitelisting valid primer pairs and demuxing by patient

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May 16, 2020, 10:56:36 AM5/16/20

to SMRT_covid19

CoSA now at v2.6.0

Added section on how to demux by patient https://github.com/Magdoll/CoSA/wiki/SARS-CoV-2-variant-calling-using-PacBio-HiFi-data#2-if-multiplexed-de-multiplex-different-patient-samples
I added a whitelist option to subsample_amplicons.py for those using amplicon primers (ex: ARTIC) where the pairing of F/R is not 1-to-1 https://github.com/Magdoll/CoSA/wiki/SARS-CoV-2-variant-calling-using-PacBio-HiFi-data#trim
Also, fixed (since v2.5.0) is the juliet json to VCF script juliet_json_to_vcf.py which did not handle multi-SNP in a single codon properly
Added a new section on consensus calling using ConsensusFixer. Downside is it is not really maintained anymore (although it is written by our own Armin T at his previous position) https://github.com/Magdoll/CoSA/wiki/SARS-CoV-2-variant-calling-using-PacBio-HiFi-data#option-3-use-consensusfixer