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sanger-tol / variantcalling

This Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite but with options to run on unaligned reads.
https://pipelines.tol.sanger.ac.uk/variantcalling
MIT License
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Nf-core module: samtools_view #15

Closed priyanka-surana closed 2 years ago

priyanka-surana commented 2 years ago

Description of feature

Convert the CRAM file to either BAM or SAM depending on the most preferred input by the different subworkflows.