A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Samtools sort has been able to read more than BAM for a long time, hence "samtools view -bS | samtools sort ..." is just an unnecessary CPU consuming command.
I tested both the outputs (with and without 'samtools view -bS') and results are same for both.
Samtools sort has been able to read more than BAM for a long time, hence "samtools view -bS | samtools sort ..." is just an unnecessary CPU consuming command.
I tested both the outputs (with and without 'samtools view -bS') and results are same for both.