This nextflow script allows you to desalign and realign your BAM files in order to precisely control the alignment.
This pipeline use an optimized combination of samtools, bwa mem and sambamba in one command line with pipes.
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bam realignment with samtools, bwa and sambamba
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IARCbioinfo/bam_realignment-nf
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bam realignment with samtools, bwa and sambamba
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