Mercurial > repos > artbio > artbio_bam_cleaning
view test-data/npipe.sh @ 8:b12e50bcddd2 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 710fd3796d363d7c1b2bf87793b0c31de62e8d71"
author | artbio |
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date | Thu, 30 Dec 2021 19:53:07 +0000 |
parents | 745f529127b8 |
children |
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input="chr22_sample" && \ genome="chr22.fa" samtools index $input".bam" && \ sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped) and not(duplicate)' -f 'bam' ${input}".bam" \ | bamleftalign --fasta-reference $genome -c --max-iterations "5" - \ | samtools calmd -C 50 -b -@ 8 - $genome > $input".filt1.dedup.bamleft.calmd.bam" && \ sambamba view -h -t 8 --filter='mapping_quality <= 254' -f 'bam' -o $input".filt1.dedup.bamleft.calmd.filt2.bam" $input".filt1.dedup.bamleft.calmd.bam"