# HG changeset patch
# User youyuh48
# Date 1566712731 14400
# Node ID ee65e517769dfc5540fb9b58e00a87537de13a4c
planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
diff -r 000000000000 -r ee65e517769d sniffles.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sniffles.xml Sun Aug 25 01:58:51 2019 -0400
@@ -0,0 +1,142 @@
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+ Structural variation caller using third generation sequencing
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+ sniffles
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+ -v
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+Input/Output:
+ -m , --mapped_reads
+ (required) Sorted bam File
+ -v , --vcf
+ VCF output file name []
+ -b , --bedpe
+ bedpe output file name []
+ \--Ivcf
+ Input VCF file name. Enable force calling []
+ \--tmp_file
+ path to temporary file otherwise Sniffles will use the current directory. []
+
+General:
+ -s , --min_support
+ Minimum number of reads that support a SV. [10]
+ \--max_num_splits
+ Maximum number of splits per read to be still taken into account. [7]
+ -d , --max_distance
+ Maximum distance to group SV together. [1000]
+ -t , --threads
+ Number of threads to use. [3]
+ -l , --min_length
+ Minimum length of SV to be reported. [30]
+ -q , --minmapping_qual
+ Minimum Mapping Quality. [20]
+ -n , --num_reads_report
+ Report up to N reads that support the SV in the vcf file. -1: report all. [0]
+ -r , --min_seq_size
+ Discard read if non of its segment is larger then this. [2000]
+ -z , --min_zmw
+ Discard SV that are not supported by at least x zmws. This applies only for PacBio recognizable reads. [0]
+ \--cs_string
+ Enables the scan of CS string instead of Cigar and MD. [false]
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+Clustering/phasing and genotyping:
+ \--genotype
+ Enables Sniffles to compute the genotypes. [false]
+ \--cluster
+ Enables Sniffles to phase SVs that occur on the same reads [false]
+ \--cluster_support
+ Minimum number of reads supporting clustering of SV. [1]
+ -f , --allelefreq
+ Threshold on allele frequency (0-1). [0]
+ \--min_homo_af
+ Threshold on allele frequency (0-1). [0.8]
+ \--min_het_af
+ Threshold on allele frequency (0-1). [0.3]
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+Advanced:
+ \--report_BND
+ Dont report BND instead use Tra in vcf output. [true]
+ \--report_seq
+ Report sequences for indels in vcf output. (Beta version!) [false]
+ \--ignore_sd
+ Ignores the sd based filtering. [false]
+ \--report_read_strands
+ Enables the report of the strand categories per read. (Beta) [false]
+ \--ccs_reads
+ Preset CCS Pacbio setting. (Beta) [false]
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+Parameter estimation:
+ \--skip_parameter_estimation
+ Enables the scan if only very few reads are present. [false]
+ \--del_ratio
+ Estimated ration of deletions per read (0-1). [0.0458369]
+ \--ins_ratio
+ Estimated ratio of insertions per read (0-1). [0.049379]
+ \--max_diff_per_window
+ Maximum differences per 100bp. [50]
+ \--max_dist_aln_events
+ Maximum distance between alignment (indel) events. [4]
+ ]]>
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+
+ 10.1038/s41592-018-0001-7
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diff -r 000000000000 -r ee65e517769d test-data/expected_output.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_output.vcf Sun Aug 25 01:58:51 2019 -0400
@@ -0,0 +1,118 @@
+##fileformat=VCFv4.2
+##source=Sniffles
+##fileDate=20180307
+##contig=
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+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_region.bam
+21 21492142 0 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.8;CHR2=21;END=21492648;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=0.572582;Kurtosis_quant_stop=1.417662;SVTYPE=DEL;SUPTYPE=AL,SR;SVLEN=506;STRANDS=+-;RE=48 GT:DR:DV ./.:.:48
diff -r 000000000000 -r ee65e517769d test-data/reads_region.bam
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