Mercurial > repos > nml > filter_vcf
annotate test-data/filterVcf.output.1.vcf @ 1:48922d9ca355 draft default tip
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
| author | nml |
|---|---|
| date | Tue, 23 Jun 2020 10:26:18 -0400 |
| parents | 93ea196681c8 |
| children |
| rev | line source |
|---|---|
|
0
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
1 ##fileformat=VCFv4.1 |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
2 ##fileDate=20140423 |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
3 ##source=freeBayes version 0.9.8 |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
4 ##reference=/home/aaron/microbialinformatics2014/core-snv-tutorial/output-10-subsample/reference/2010EL-1749.2010EL-1786-c1_2000_2400kb.fasta |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
5 ##phasing=none |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
6 ##commandline="/opt/freebayes/freebayes --bam /home/aaron/microbialinformatics2014/core-snv-tutorial/output-10-subsample/bam/2010EL-1749.bam --vcf /home/aaron/microbialinformatics2014/core-snv-tutorial/output-10-subsample/vcf/2010EL-1749.vcf --fasta-reference /home/aaron/microbialinformatics2014/core-snv-tutorial/output-10-subsample/reference/2010EL-1749.2010EL-1786-c1_2000_2400kb.fasta --min-coverage 2 --pvar 0 --ploidy 1 --left-align-indels --min-mapping-quality 30 --min-base-quality 30 --min-alternate-fraction 0.75" |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
7 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
8 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
9 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
10 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
11 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
12 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observations"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
13 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
14 ##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
15 ##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
16 ##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
17 ##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
18 ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
19 ##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
20 ##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
21 ##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
22 ##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
23 ##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
24 ##INFO=<ID=XRM,Number=1,Type=Float,Description="Reference allele read mismatch rate: The rate of SNVs + MNPs + INDELs in reads supporting the reference allele."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
25 ##INFO=<ID=XRS,Number=1,Type=Float,Description="Reference allele read SNV rate: The rate of per-base mismatches (SNVs + MNPs) in reads supporting the reference allele."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
26 ##INFO=<ID=XRI,Number=1,Type=Float,Description="Reference allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the reference allele."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
27 ##INFO=<ID=XAM,Number=A,Type=Float,Description="Alternate allele read mismatch rate: The rate of SNVs + MNPs + INDELs in reads supporting the alternate allele, excluding the called variant."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
28 ##INFO=<ID=XAS,Number=A,Type=Float,Description="Alternate allele read SNV rate: The rate of per-base mismatches (SNVs + MNPs) in reads supporting the alternate allele, excluding the called variant."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
29 ##INFO=<ID=XAI,Number=A,Type=Float,Description="Alternate allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the alternate allele, excluding the called variant."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
30 ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
31 ##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination in the posterior is variant (non homozygous)."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
32 ##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or CpA)"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
33 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snv, mnp, ins, del, or complex."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
34 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
35 ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
36 ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
37 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Phred-scaled discrete HWE prior probability of the genotyping across all samples."> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
38 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
39 ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
40 ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
41 ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
42 ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
43 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
44 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
45 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
46 ##FORMAT=<ID=GLE,Number=1,Type=String,Description="Genotype Likelihood Explicit, same as GL, but with tags to indicate the specific genotype. For instance, 0^-75.22|1^-223.42|0/0^-323.03|1/0^-99.29|1/1^-802.53 represents both haploid and diploid genotype likilehoods in a biallelic context"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
47 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
48 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
49 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
50 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
51 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
52 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
53 gi|360034408|ref|NC_016445.1|_2000000_2400000 128 . G A 197.867 . AB=0;ABP=0;AC=1;AF=1;AN=1;AO=3;CIGAR=1X;DP=3;DPRA=0;EPP=3.73412;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=54;MQMR=0;NS=1;NUMALT=1;ODDS=45.5605;PAIRED=0;PAIREDR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAP=3.73412;SRP=0;TYPE=snv;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1:50000:3:0:0:3:212:-19.7867,0 |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
54 gi|360034408|ref|NC_016445.1|_2000000_2400000 129 . A T 197.867 . AB=0;ABP=0;AC=1;AF=1;AN=1;AO=3;CIGAR=1X;DP=3;DPRA=0;EPP=3.73412;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=54;MQMR=0;NS=1;NUMALT=1;ODDS=45.5605;PAIRED=0;PAIREDR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAP=3.73412;SRP=0;TYPE=snv;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1:50000:3:0:0:3:212:-19.7867,0 |
|
93ea196681c8
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff
changeset
|
55 gi|360034408|ref|NC_016445.1|_2000000_2400000 256 . A C 250.1 . AB=0;ABP=0;AC=1;AF=1;AN=1;AO=6;CIGAR=1X;DP=8;DPRA=0;EPP=8.80089;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=54;MQMR=54;NS=1;NUMALT=1;ODDS=57.5877;PAIRED=0;PAIREDR=0;RO=2;RPP=8.80089;RPPR=7.35324;RUN=1;SAP=4.45795;SRP=3.0103;TYPE=snv;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1:50000:8:2:142:6:420:-38.5,-13.49 |