Mercurial > repos > devteam > freebayes
comparison test-data/freebayes-phix174-test3.vcf @ 30:ef2c525bd8cd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
| author | iuc |
|---|---|
| date | Wed, 06 Nov 2019 17:02:57 -0500 |
| parents | 9f164587a92f |
| children | 8a7a42541080 |
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| 29:156b60c1530f | 30:ef2c525bd8cd |
|---|---|
| 1 ##fileformat=VCFv4.2 | 1 ##fileformat=VCFv4.2 |
| 2 ##fileDate=20191031 | |
| 3 ##source=freeBayes v1.3.1-dirty | |
| 2 ##reference=localref.fa | 4 ##reference=localref.fa |
| 3 ##contig=<ID=phiX174,length=5386> | 5 ##contig=<ID=phiX174,length=5386> |
| 4 ##phasing=none | 6 ##phasing=none |
| 5 ##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic --standard-filters --min-coverage 14" | 7 ##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf --min-coverage 14 --skip-coverage 0 --limit-coverage 0 --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0.05 --pooled-continuous --report-monomorphic --standard-filters" |
| 6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> | 8 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> |
| 7 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> | 9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> |
| 8 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> | 10 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> |
| 9 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> | 11 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> |
| 10 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | 12 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> |