Mercurial > repos > matthias > sam_to_bam
comparison samtools_mpileup/test-data/samtools_mpileup_out_4.vcf @ 0:c1af49d0c445 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
| author | matthias |
|---|---|
| date | Fri, 22 Feb 2019 16:01:53 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:c1af49d0c445 |
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| 1 ##fileformat=VCFv4.2 | |
| 2 ##FILTER=<ID=PASS,Description="All filters passed"> | |
| 3 ##samtoolsVersion=1.1+htslib-1.1 | |
| 4 ##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /var/galaxy/workspace/CleanGalaxy/tool-data/phiX/sam_indexes/phiX/phiX.fa -C 0 -d 200 -E -q 0 -Q 43 -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_756.dat /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_755.dat | |
| 5 ##reference=file:///var/galaxy/workspace/CleanGalaxy/tool-data/phiX/sam_indexes/phiX/phiX.fa | |
| 6 ##contig=<ID=phiX174,length=5386> | |
| 7 ##ALT=<ID=X,Description="Represents allele(s) other than observed."> | |
| 8 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> | |
| 9 ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> | |
| 10 ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> | |
| 11 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> | |
| 12 ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> | |
| 13 ##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> | |
| 14 ##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> | |
| 15 ##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> | |
| 16 ##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> | |
| 17 ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> | |
| 18 ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> | |
| 19 ##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h"> | |
| 20 ##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling"> | |
| 21 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> | |
| 22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /tmp/tmp5TzrZC/tmpDtGVov/database/files/000/dataset_755.dat |