To ensure consistency in major updates to the CG workflow, this PR includes changes parallel to this PR. In particular, "The minimum depth parameter in samtools pileup is approximate since it discards whole reads (rather than applying the truncation separately at each position the read spans). This appears to especially cause bad behavior for some amplicon library preps, where overlapping regions between amplicons can cause nearly all reads to be discarded at the 5' end of an amplicon."
Additionally, we remove two pipeline steps that are extraneous to the primary pipeline goal of generating consensus genomes - RealignConsensus and IntrahostVariants - to streamline the pipeline.
The changes have been tested on five samples (ARTIC v3 and MSSPE). Results are as expected.
To ensure consistency in major updates to the CG workflow, this PR includes changes parallel to this PR. In particular, "The minimum depth parameter in samtools pileup is approximate since it discards whole reads (rather than applying the truncation separately at each position the read spans). This appears to especially cause bad behavior for some amplicon library preps, where overlapping regions between amplicons can cause nearly all reads to be discarded at the 5' end of an amplicon."
Additionally, we remove two pipeline steps that are extraneous to the primary pipeline goal of generating consensus genomes -
RealignConsensusandIntrahostVariants- to streamline the pipeline.The changes have been tested on five samples (ARTIC v3 and MSSPE). Results are as expected.