Mercurial > repos > iuc > irissv
comparison test-data/test_out.vcf @ 0:30fc9f2bcbe4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
| author | iuc |
|---|---|
| date | Tue, 19 Jan 2021 20:30:21 +0000 |
| parents | |
| children | 3242dbeea69c |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:30fc9f2bcbe4 |
|---|---|
| 1 ##fileformat=VCFv4.1 | |
| 2 ##source=Sniffles | |
| 3 ##fileDate=20190906 | |
| 4 ##contig=<ID=chr1,length=110720> | |
| 5 ##ALT=<ID=DEL,Description="Deletion"> | |
| 6 ##ALT=<ID=DUP,Description="Duplication"> | |
| 7 ##ALT=<ID=INV,Description="Inversion"> | |
| 8 ##ALT=<ID=INVDUP,Description="InvertedDUP with unknown boundaries"> | |
| 9 ##ALT=<ID=TRA,Description="Translocation"> | |
| 10 ##ALT=<ID=INS,Description="Insertion"> | |
| 11 ##FILTER=<ID=UNRESOLVED,Description="An insertion that is longer than the read and thus we cannot predict the full size."> | |
| 12 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation"> | |
| 13 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant"> | |
| 14 ##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends"> | |
| 15 ##INFO=<ID=RE,Number=1,Type=Integer,Description="read support"> | |
| 16 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> | |
| 17 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation"> | |
| 18 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV"> | |
| 19 ##INFO=<ID=REF_strand,Number=2,Type=Integer,Description="Length of the SV"> | |
| 20 ##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV"> | |
| 21 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
| 22 ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of reads supporting SVs (comma separated)"> | |
| 23 ##INFO=<ID=SEQ,Number=1,Type=String,Description="Extracted sequence from the best representative read."> | |
| 24 ##INFO=<ID=STD_quant_start,Number=A,Type=Float,Description="STD of the start breakpoints across the reads."> | |
| 25 ##INFO=<ID=STD_quant_stop,Number=A,Type=Float,Description="STD of the stop breakpoints across the reads."> | |
| 26 ##INFO=<ID=Kurtosis_quant_start,Number=A,Type=Float,Description="Kurtosis value of the start breakpoints across the reads."> | |
| 27 ##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=Float,Description="Kurtosis value of the stop breakpoints across the reads."> | |
| 28 ##INFO=<ID=SUPTYPE,Number=A,Type=String,Description="Type by which the variant is supported.(SR,ALN,NR)"> | |
| 29 ##INFO=<ID=STRANDS,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> | |
| 30 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency."> | |
| 31 ##INFO=<ID=ZMW,Number=A,Type=Integer,Description="Number of ZMWs (Pacbio) supporting SV."> | |
| 32 ##INFO=<ID=IRIS_PROCESSED,Number=1,Type=String,Description="Whether or not a variant has been considered by Iris for refinement"> | |
| 33 ##INFO=<ID=IRIS_REFINED,Number=1,Type=String,Description="Whether or not a variant has been refined by Iris"> | |
| 34 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 35 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads"> | |
| 36 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads"> | |
| 37 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT aln_sorted.bam | |
| 38 chr1 6932 0 A ATGGGGGGAGGCCCCCCCCGGGGGGGGGCCCCCCCCAGGGGGGGGGCCCCCCCCGGGGGGGGCCCCCCCCCGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=chr1;END=6932;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=76;STRANDS=+-;RE=32;REF_strand=32;AF=1;IRIS_PROCESSED=1;IRIS_REFINED=1 GT:DR:DV 1/1:0:32 | |
| 39 chr1 13790 1 CACCATGTTGGCCAAGATGTTCTCGATCTCCTGACCTTGTGATCTGCCTGCCTCGTCCTCCCAAAGTGCTG C . 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;IRIS_PROCESSED=1;IRIS_REFINED=0 GT:DR:DV 1/1:0:45 |