# HG changeset patch
# User artbio
# Date 1598369702 14400
# Node ID ee8fc44b16552a1d424467923ee50873dd97c26b
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
diff -r 000000000000 -r ee8fc44b1655 lumpy_smoove.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lumpy_smoove.xml Tue Aug 25 11:35:02 2020 -0400
@@ -0,0 +1,186 @@
+
+ find structural variants using the smoove workflow
+
+ macro_lumpy_smoove.xml
+
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+ smoove
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+**smoove** simplifies and speeds calling and genotyping SVs for short reads. It also improves
+specificity by removing many spurious alignment signals that are indicative of low-level
+noise and often contribute to spurious calls.
+
+There is a blog-post describing smoove in more detail
+here: https://brentp.github.io/post/smoove/
+
+Currently, this Galaxy tool only wraps smoove for 2 samples (bam normal and tumor inputs),
+which translates in the command line::
+
+
+
+Note that the --genotype option which allows to stream smoove to svtyper is not implemented
+due to an error returned by svtyper in the smoove conda environment
+
+the --exclude $bed is highly recommended as it can be used to ignore reads that overlap
+problematic regions.
+
+A good set of regions for GRCh37 is https://github.com/hall-lab/speedseq/blob/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed
+
+And for hg38 https://github.com/hall-lab/speedseq/blob/master/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed
+
+smoove will::
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+ 1. parallelize calls to lumpy_filter to extract split and discordant reads required by lumpy
+
+ 2. further filter lumpy_filter calls to remove high-coverage, spurious regions and user-specified chroms like 'hs37d5';
+ it will also remove reads that we've found are likely spurious signals. after this, it will
+ remove singleton reads (where the mate was removed by one of the previous filters)
+ from the discordant bams. This makes lumpy much faster and less memory-hungry.
+
+ 3. calculate per-sample metrics for mean, standard deviation, and distribution of insert
+ size as required by lumpy.
+
+ 4. stream output of lumpy directly into multiple svtyper processes for parallel-by-region
+ genotyping while lumpy is still running. This option in not currently implemented in Galaxy
+
+ 5. sort, compress, and index final VCF.
+
+**Input(s)**
+
+
+*BAM files*: One Bam for normal sample and one Bam for tumor sample.
+Only BAM alignments produced by BWA-mem have been tested with this tool
+
+*A bed file* describing the regions to exclude from the analysis
+
+
+*Additional options*: refer to smoove GitHub repository_ and the lumpy publication (doi 10.1186/gb-2014-15-6-r84)
+
+.. _repository: https://github.com/brentp/smoove
+
+
+Options::
+
+ (compress) -> index ]
+ [Y] gsort [(sort) -> compress -> index ]
+ [Y] tabix [ sort -> compress -> (index)]
+ [Y] lumpy
+ [Y] lumpy_filter
+ [Y] samtools
+ [Y] svtyper
+ [Y] mosdepth [extra filtering of split and discordant files for better scaling]
+
+ [Y] duphold [(optional) annotate calls with depth changes]
+ [Y] svtools [only needed for large cohorts].
+
+ Available sub-commands are below. Each can be run with -h for additional help.
+
+ call : call lumpy (and optionally svtyper)
+ merge : merge and sort (using svtools) calls from multiple samples
+ genotype : parallelize svtyper on an input VCF
+ paste : square final calls from multiple samples (each with same number of variants)
+ plot-counts : plot counts of split, discordant reads before, after smoove filtering
+ annotate : annotate a VCF with gene and quality of SV call
+ hipstr : run hipSTR in parallel
+ cnvnator : run cnvnator in parallel
+ duphold : run duphold in parallel (this can be done by adding a flag to call or genotype)
+ ]]>
+
+
+
+ 10.1186/gb-2014-15-6-r84
+
+
diff -r 000000000000 -r ee8fc44b1655 macro_lumpy_smoove.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macro_lumpy_smoove.xml Tue Aug 25 11:35:02 2020 -0400
@@ -0,0 +1,35 @@
+
+
+
+ &1 || echo "Error running samtools faidx for lumpy_smoove" >&2 &&
+ #else:
+ ln -s '${source.index.fields.path}' reference.fa &&
+ ln -s '${source.index.fields.path}.fai' reference.fa.fai &&
+ #end if
+ ]]>
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