Mercurial > repos > artbio > artbio_bam_cleaning

annotate test-data/npipe.sh @ 12:b0f65f88411f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning commit 6a7ed08b76a45cfcda4e030163d9f246163934ed
author artbio
date Tue, 10 Oct 2023 11:14:10 +0000
parents 745f529127b8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents:
diff changeset
1 input="chr22_sample" && \
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents:
diff changeset
2 genome="chr22.fa"
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents:
diff changeset
3 samtools index $input".bam" && \
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents:
diff changeset
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" \
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents:
diff changeset
5 | bamleftalign --fasta-reference $genome -c --max-iterations "5" - \
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents:
diff changeset
6 | samtools calmd -C 50 -b -@ 8 - $genome > $input".filt1.dedup.bamleft.calmd.bam" && \
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents:
diff changeset
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"
745f529127b8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit b782130b62b7c74911774b58c7a965a99dee1519"
artbio
parents:
diff changeset
8