Mercurial > repos > devteam > samtools_mpileup

annotate test-data/samtools_mpileup_out_2.vcf @ 3:da0203c3461a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
author devteam
date Fri, 11 Sep 2015 14:16:52 -0400
parents
children 483949f5c3b0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
1 ##fileformat=VCFv4.2
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
2 ##FILTER=<ID=PASS,Description="All filters passed">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
3 ##samtoolsVersion=1.1+htslib-1.1
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
4 ##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_736.dat /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
5 ##reference=file:///tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
6 ##contig=<ID=phiX174,length=5386>
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
7 ##ALT=<ID=X,Description="Represents allele(s) other than observed.">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
8 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
9 ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
10 ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
11 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
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">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
13 ##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
14 ##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
15 ##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
16 ##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
17 ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
18 ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
19 ##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
20 ##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
21 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
da0203c3461a planemo upload commit 9c291d7ad7c82e6051fe3e5ddffbe7a5edf6f006
devteam
parents:
diff changeset
22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat