Mercurial > repos > artbio > artbio_bam_cleaning

comparison test-data/npipe.sh @ 7:745f529127b8 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
author artbio
date Mon, 20 Dec 2021 19:44:29 +0000
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6:999c2b871f36 7:745f529127b8
1 input="chr22_sample" && \
2 genome="chr22.fa"
3 samtools index $input".bam" && \
4 sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped) and not(duplicate)' -f 'bam' ${input}".bam" \
5 | bamleftalign --fasta-reference $genome -c --max-iterations "5" - \
6 | samtools calmd -C 50 -b -@ 8 - $genome > $input".filt1.dedup.bamleft.calmd.bam" && \
7 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"
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