Mercurial > repos > iuc > snpfreqplot
diff test-data/no_variants.vcf @ 2:dc51db22310c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
| author | iuc |
|---|---|
| date | Fri, 18 Dec 2020 23:48:01 +0000 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/no_variants.vcf Fri Dec 18 23:48:01 2020 +0000 @@ -0,0 +1,24 @@ +##fileformat=VCFv4.0 +##fileDate=20200707 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb02/galaxy_db/job_working_directory/009/430/9430166/working/pp-tmp/lofreq2_call_parallelpfou9vt9/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_66,Description="Minimum SNV Quality (Phred) 66"> +##FILTER=<ID=min_indelqual_52,Description="Minimum Indel Quality (Phred) 52"> +##FILTER=<ID=min_snvqual_70,Description="Minimum SNV Quality (Phred) 70"> +##FILTER=<ID=min_indelqual_57,Description="Minimum Indel Quality (Phred) 57"> +##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000"> +##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /data/dnb02/galaxy_db/job_working_directory/009/430/9430172/galaxy_dataset_24243789.dat NC_045512.2 /data/dnb02/galaxy_db/files/022/094/dataset_22094491.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +#CHROM POS ID REF ALT QUAL FILTER INFO