Mercurial > repos > artbio > artbio_bam_cleaning

comparison test-data/pipe.sh @ 0:65d6d2b554b3 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit adfad19ff505ac7baa3688997bfa9f64243aaace"
author artbio
date Fri, 02 Oct 2020 00:17:33 +0000
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-1:000000000000 0:65d6d2b554b3
1 input="match_chr21_DBA_974" && \
2 genome="chr21.fa" && \
3 samtools index $input".bam" && \
4 sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped)' -f 'bam' $input".bam" \
5 | samtools rmdup - - \
6 tee $input".filt1.dedup.bam"| bamleftalign --fasta-reference $genome -c --max-iterations "5" - \
7 | samtools calmd -C 50 -b -@ 4 - $genome > $input".filt1.dedup.bamleft.calmd.bam" && \
8 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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