Mercurial > repos > iuc > sniffles
view test-data/expected_output.vcf @ 4:43fffeed243f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 03fbb13717809f9198ab113192d241599705ef7b
author | iuc |
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date | Sun, 29 Sep 2024 10:23:36 +0000 |
parents | 09f5c6f3088a |
children |
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##fileformat=VCFv4.2 ##source=Sniffles2_2.4 ##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/2/outputs/dataset_c3cc0dff-254a-4e6b-837f-fa8a4db7f051.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --detect-large-ins 0 --cluster-binsize 100 --cluster-r 2.5" ##fileDate="2024/09/28 23:18:28" ##contig=<ID=1,length=249250621> ##contig=<ID=2,length=243199373> ##contig=<ID=3,length=198022430> ##contig=<ID=4,length=191154276> ##contig=<ID=5,length=180915260> ##contig=<ID=6,length=171115067> ##contig=<ID=7,length=159138663> ##contig=<ID=8,length=146364022> ##contig=<ID=9,length=141213431> ##contig=<ID=10,length=135534747> ##contig=<ID=11,length=135006516> ##contig=<ID=12,length=133851895> ##contig=<ID=13,length=115169878> ##contig=<ID=14,length=107349540> ##contig=<ID=15,length=102531392> ##contig=<ID=16,length=90354753> ##contig=<ID=17,length=81195210> ##contig=<ID=18,length=78077248> ##contig=<ID=19,length=59128983> ##contig=<ID=20,length=63025520> ##contig=<ID=21,length=48129895> ##contig=<ID=22,length=51304566> ##contig=<ID=X,length=155270560> ##contig=<ID=Y,length=59373566> ##contig=<ID=MT,length=16569> ##contig=<ID=GL000207.1,length=4262> ##contig=<ID=GL000226.1,length=15008> ##contig=<ID=GL000229.1,length=19913> ##contig=<ID=GL000231.1,length=27386> ##contig=<ID=GL000210.1,length=27682> ##contig=<ID=GL000239.1,length=33824> ##contig=<ID=GL000235.1,length=34474> ##contig=<ID=GL000201.1,length=36148> ##contig=<ID=GL000247.1,length=36422> ##contig=<ID=GL000245.1,length=36651> ##contig=<ID=GL000197.1,length=37175> ##contig=<ID=GL000203.1,length=37498> ##contig=<ID=GL000246.1,length=38154> ##contig=<ID=GL000249.1,length=38502> ##contig=<ID=GL000196.1,length=38914> ##contig=<ID=GL000248.1,length=39786> ##contig=<ID=GL000244.1,length=39929> ##contig=<ID=GL000238.1,length=39939> ##contig=<ID=GL000202.1,length=40103> ##contig=<ID=GL000234.1,length=40531> ##contig=<ID=GL000232.1,length=40652> ##contig=<ID=GL000206.1,length=41001> ##contig=<ID=GL000240.1,length=41933> ##contig=<ID=GL000236.1,length=41934> ##contig=<ID=GL000241.1,length=42152> ##contig=<ID=GL000243.1,length=43341> ##contig=<ID=GL000242.1,length=43523> ##contig=<ID=GL000230.1,length=43691> ##contig=<ID=GL000237.1,length=45867> ##contig=<ID=GL000233.1,length=45941> ##contig=<ID=GL000204.1,length=81310> ##contig=<ID=GL000198.1,length=90085> ##contig=<ID=GL000208.1,length=92689> ##contig=<ID=GL000191.1,length=106433> ##contig=<ID=GL000227.1,length=128374> ##contig=<ID=GL000228.1,length=129120> ##contig=<ID=GL000214.1,length=137718> ##contig=<ID=GL000221.1,length=155397> ##contig=<ID=GL000209.1,length=159169> ##contig=<ID=GL000218.1,length=161147> ##contig=<ID=GL000220.1,length=161802> ##contig=<ID=GL000213.1,length=164239> ##contig=<ID=GL000211.1,length=166566> ##contig=<ID=GL000199.1,length=169874> ##contig=<ID=GL000217.1,length=172149> ##contig=<ID=GL000216.1,length=172294> ##contig=<ID=GL000215.1,length=172545> ##contig=<ID=GL000205.1,length=174588> ##contig=<ID=GL000219.1,length=179198> ##contig=<ID=GL000224.1,length=179693> ##contig=<ID=GL000223.1,length=180455> ##contig=<ID=GL000195.1,length=182896> ##contig=<ID=GL000212.1,length=186858> ##contig=<ID=GL000222.1,length=186861> ##contig=<ID=GL000200.1,length=187035> ##contig=<ID=GL000193.1,length=189789> ##contig=<ID=GL000194.1,length=191469> ##contig=<ID=GL000225.1,length=211173> ##contig=<ID=GL000192.1,length=547496> ##contig=<ID=NC_007605,length=171823> ##contig=<ID=hs37d5,length=35477943> ##ALT=<ID=INS,Description="Insertion"> ##ALT=<ID=DEL,Description="Deletion"> ##ALT=<ID=DUP,Description="Duplication"> ##ALT=<ID=INV,Description="Inversion"> ##ALT=<ID=BND,Description="Breakend; Translocation"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="Number of reference reads"> ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of variant reads"> ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase-block, zero if none or not phased"> ##FORMAT=<ID=ID,Number=1,Type=String,Description="Individual sample SV ID for multi-sample output"> ##FILTER=<ID=PASS,Description="All filters passed"> ##FILTER=<ID=GT,Description="Genotype filter"> ##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter"> ##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter"> ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter"> ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter"> ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)"> ##FILTER=<ID=COV_CHANGE,Description="Coverage change filter"> ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS"> ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start"> ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center"> ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end"> ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream"> ##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter"> ##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic"> ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter"> ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs"> ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs"> ##FILTER=<ID=STRAND_MOSAIC,Description="Strand support filter for mosaic SVs"> ##FILTER=<ID=SVLEN_MIN,Description="SV length filter"> ##FILTER=<ID=SVLEN_MIN_MOSAIC,Description="SV length filter for mosaic SVs"> ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Structural variation with precise breakpoints"> ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Structural variation with imprecise breakpoints"> ##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Structural variation classified as putative mosaic"> ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation"> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variation"> ##INFO=<ID=CHR2,Number=1,Type=String,Description="Mate chromsome for BND SVs"> ##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description="Number of reads supporting the structural variation"> ##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description="Number of reads supporting an INS/DEL SV (non-split events only)"> ##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description="Number of soft-clipped reads putatively supporting the long insertion SV"> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation"> ##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description="Standard deviation of structural variation start position"> ##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description="Standard deviation of structural variation length"> ##INFO=<ID=COVERAGE,Number=.,Type=Float,Description="Coverages near upstream, start, center, end, downstream of structural variation"> ##INFO=<ID=STRAND,Number=1,Type=String,Description="Strands of supporting reads for structural variant"> ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count, summed up over all samples"> ##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples"> ##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence"> ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)"> ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> ##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads"> ##INFO=<ID=PHASE,Number=.,Type=String,Description="Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE 21 21492142 Sniffles2.DEL.0S14 N <DEL> 52 PASS PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;AF=1.000;STDEV_LEN=0.509;STDEV_POS=1.404 GT:GQ:DR:DV 1/1:60:0:48