Mercurial > repos > iuc > sniffles
diff test-data/expected_outcome5.vcf @ 5:ceff2f6a5368 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit a2dd716a67d60533534269faef8e87e30496bce0
| author | iuc |
|---|---|
| date | Thu, 14 Nov 2024 07:25:22 +0000 |
| parents | 43fffeed243f |
| children |
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--- a/test-data/expected_outcome5.vcf Sun Sep 29 10:23:36 2024 +0000 +++ b/test-data/expected_outcome5.vcf Thu Nov 14 07:25:22 2024 +0000 @@ -1,7 +1,7 @@ ##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/000/10/outputs/dataset_a9aaaabe-54e2-4f60-9a73-0454076bd7c5.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --mosaic" -##fileDate="2024/09/28 23:21:10" +##source=Sniffles2_2.5 +##command="/home/ross/miniconda3/envs/__sniffles@2.5.2/bin/sniffles -t 1 -i input.bam -v /tmp/tmpqwecq14c/job_working_directory/000/10/outputs/dataset_0e92fd8e-42f6-4ba5-a5f3-5ec578798305.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --mosaic" +##fileDate="2024/11/13 10:05:00" ##contig=<ID=1,length=249250621> ##contig=<ID=2,length=243199373> ##contig=<ID=3,length=198022430> @@ -106,14 +106,15 @@ ##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_DEL,Description="Coverage change filter for DEL"> +##FILTER=<ID=COV_CHANGE_DUP,Description="Coverage change filter for DUP"> ##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=MOSAIC_VAF,Description="Mosaic variant allele fraction filter"> +##FILTER=<ID=NOT_MOSAIC_VAF,Description="Variant allele fraction 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"> @@ -138,7 +139,7 @@ ##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=VAF,Number=1,Type=Float,Description="Variant Allele Fraction"> ##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