Mercurial > repos > iuc > samtools_ampliconclip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
author iuc
date Mon, 27 Jun 2022 20:07:59 +0000
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samtools ampliconclip -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.clipped.bam
samtools ampliconclip --strand -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.clipped.strand.bam
samtools ampliconclip --hard-clip -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.hardclipped.bam
samtools ampliconclip --both-ends --no-excluded --strand --fail-len 30 -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.clipped.strand_gt30.bam