Mercurial > repos > youyuh48 > sniffles

diff test-data/expected_output.vcf @ 0:ee65e517769d draft

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planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
author youyuh48
date Sun, 25 Aug 2019 01:58:51 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/expected_output.vcf	Sun Aug 25 01:58:51 2019 -0400
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+##fileformat=VCFv4.2
+##source=Sniffles
+##fileDate=20180307
+##contig=<ID=1,length=249250621>
+##contig=<ID=2,length=243199373>
+##contig=<ID=3,length=198022430>
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+##contig=<ID=NC_007605,length=171823>
+##contig=<ID=hs37d5,length=35477943>
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=INVDUP,Description="InvertedDUP with unknown boundaries">
+##ALT=<ID=TRA,Description="Translocation">
+##ALT=<ID=INS,Description="Insertion">
+##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
+##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
+##INFO=<ID=RE,Number=1,Type=Integer,Description="read support">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV">
+##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=STD_quant_start,Number=A,Type=Integer,Description="STD of the start breakpoints across the reads.">
+##INFO=<ID=STD_quant_stop,Number=A,Type=Integer,Description="STD of the stop breakpoints across the reads.">
+##INFO=<ID=Kurtosis_quant_start,Number=A,Type=Integer,Description="Kurtosis value of the start breakpoints accross the reads.">
+##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=Integer,Description="Kurtosis value of the stop breakpoints accross the reads.">
+##INFO=<ID=SUPTYPE,Number=1,Type=String,Description="Type by which the variant is supported.(SR,ALN)">
+##INFO=<ID=SUPTYPE,Number=1,Type=String,Description="Type by which the variant is supported.(SR,ALN)">
+##INFO=<ID=STRANDS,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency.">
+##INFO=<ID=ZMW,Number=A,Type=Integer,Description="Number of ZMWs (Pacbio) supporting SV.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	reads_region.bam
+21	21492142	0	N	<DEL>	.	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