Mercurial > repos > iuc > samtools_ampliconclip
diff test-data/rebuild_output_bams.sh @ 0:a941babb9268 draft
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 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rebuild_output_bams.sh Mon Jun 27 20:07:59 2022 +0000 @@ -0,0 +1,4 @@ +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