Mercurial > repos > artbio > artbio_bam_cleaning

view test-data/pipe.sh @ 1:b550841f568b draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 2d441fd84bf17c0899d0b57ea35c84cb83b77119"
author artbio
date Thu, 08 Oct 2020 14:55:04 +0000
parents 65d6d2b554b3
children
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input="match_chr21_DBA_974" && \
genome="chr21.fa" && \
samtools index $input".bam" && \
sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped)' -f 'bam' $input".bam" \
| samtools rmdup - - \
tee $input".filt1.dedup.bam"| bamleftalign --fasta-reference $genome -c --max-iterations "5" - \
| samtools calmd  -C 50 -b -@ 4 - $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"