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annotate test-data/sniffles.vcf @ 2:b4b6b660293a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
author iuc
date Wed, 06 Jul 2022 07:07:21 +0000
parents 30fc9f2bcbe4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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1 ##fileformat=VCFv4.1
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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2 ##source=Sniffles
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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3 ##fileDate=20190906
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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4 ##contig=<ID=chr1,length=110720>
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5 ##ALT=<ID=DEL,Description="Deletion">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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6 ##ALT=<ID=DUP,Description="Duplication">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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7 ##ALT=<ID=INV,Description="Inversion">
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8 ##ALT=<ID=INVDUP,Description="InvertedDUP with unknown boundaries">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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9 ##ALT=<ID=TRA,Description="Translocation">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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10 ##ALT=<ID=INS,Description="Insertion">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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11 ##FILTER=<ID=UNRESOLVED,Description="An insertion that is longer than the read and thus we cannot predict the full size.">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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12 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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13 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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14 ##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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15 ##INFO=<ID=RE,Number=1,Type=Integer,Description="read support">
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16 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
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17 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
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18 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV">
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19 ##INFO=<ID=REF_strand,Number=2,Type=Integer,Description="Length of the SV">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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20 ##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
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21 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
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22 ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of reads supporting SVs (comma separated)">
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23 ##INFO=<ID=SEQ,Number=1,Type=String,Description="Extracted sequence from the best representative read.">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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24 ##INFO=<ID=STD_quant_start,Number=A,Type=Float,Description="STD of the start breakpoints across the reads.">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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25 ##INFO=<ID=STD_quant_stop,Number=A,Type=Float,Description="STD of the stop breakpoints across the reads.">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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26 ##INFO=<ID=Kurtosis_quant_start,Number=A,Type=Float,Description="Kurtosis value of the start breakpoints across the reads.">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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27 ##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=Float,Description="Kurtosis value of the stop breakpoints across the reads.">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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28 ##INFO=<ID=SUPTYPE,Number=A,Type=String,Description="Type by which the variant is supported.(SR,ALN,NR)">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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29 ##INFO=<ID=STRANDS,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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30 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency.">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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31 ##INFO=<ID=ZMW,Number=A,Type=Integer,Description="Number of ZMWs (Pacbio) supporting SV.">
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32 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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33 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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34 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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35 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT aln_sorted.bam
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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36 chr1 6930 0 N GGGGGGCGGCCCCCCCCGGGGGGGGCCCCCCCCCGGGGGGGGGCCCCCCCGCGGGGGGGGGCCCCCCCCGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=chr1;END=6930;STD_quant_start=0.000000;STD_quant_stop=1.346291;Kurtosis_quant_start=8.663097;Kurtosis_quant_stop=3.560172;SVTYPE=INS;RNAMES=CHR1_1354_+,CHR1_1732_-,CHR1_2052_-,CHR1_2093_-,CHR1_2095_+,CHR1_2109_-,CHR1_2620_+,CHR1_2797_-,CHR1_3081_-,CHR1_3198_+,CHR1_3222_-,CHR1_3277_+,CHR1_3405_+,CHR1_3951_+,CHR1_3993_+,CHR1_4076_+,CHR1_4421_+,CHR1_4453_+,CHR1_4485_-,CHR1_4606_+,CHR1_4654_-,CHR1_4663_+,CHR1_4698_+,CHR1_4981_-,CHR1_5004_+,CHR1_5087_-,CHR1_5139_+,CHR1_5805_-,CHR1_5942_-,CHR1_5979_-,CHR1_601_-,CHR1_686_-;SUPTYPE=AL,SR;SVLEN=72;STRANDS=+-;RE=32;REF_strand=32;AF=1 GT:DR:DV 1/1:0:32
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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37 chr1 13790 1 ACCATGTTGGCCAAGATGTTCTCGATCTCCTGACCTTGTGATCTGCCTGCCTCGTCCTCCCAAAGTGCTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=chr1;END=13860;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=5.511580;Kurtosis_quant_stop=7.842635;SVTYPE=DEL;RNAMES=CHR1_10314_-,CHR1_10536_-,CHR1_10726_+,CHR1_10836_-,CHR1_10943_-,CHR1_11036_+,CHR1_11496_+,CHR1_11511_+,CHR1_11624_+,CHR1_11653_-,CHR1_11724_+,CHR1_11735_-,CHR1_11742_+,CHR1_11912_+,CHR1_11924_-,CHR1_12188_+,CHR1_12517_+,CHR1_12570_-,CHR1_12685_+,CHR1_13137_+,CHR1_13143_+,CHR1_13164_+,CHR1_13172_+,CHR1_13264_+,CHR1_13410_+,CHR1_13416_+,CHR1_13449_-,CHR1_320_+,CHR1_3277_+,CHR1_4421_+,CHR1_4654_-,CHR1_5139_+,CHR1_5979_-,CHR1_7604_-,CHR1_7697_+,CHR1_7747_-,CHR1_7838_-,CHR1_8144_+,CHR1_8491_-,CHR1_8598_+,CHR1_9029_+,CHR1_9687_-,CHR1_9723_+,CHR1_9750_+,CHR1_9968_-;SUPTYPE=AL;SVLEN=-70;STRANDS=+-;RE=45;REF_strand=45;AF=1 GT:DR:DV 1/1:0:45