annotate test-data/single_variant.vcf @ 3:3d0adeee3f2b draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit c062eb1cd00ce9d565f3e2f3b042b3dd90d78ce4"

##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
NC_045512.2	241	.	C	T	13172.0	PASS	DP=363;AF=0.980716;SB=0;DP4=1,1,167,193