| Previous changeset 29:156b60c1530f (2017-10-25) Next changeset 31:57def2d7c093 (2021-11-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8" |
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modified:
freebayes.xml leftalign.xml macros.xml test-data/freebayes-phix174-test1.vcf test-data/freebayes-phix174-test2.vcf test-data/freebayes-phix174-test3.vcf test-data/freebayes-phix174-test4.vcf |
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added:
test-data/freebayes-hxb2-test5.vcf test-data/freebayes-hxb2-test6.vcf test-data/freebayes-hxb2-test7.vcf test-data/freebayes-hxb2.bam test-data/freebayes-hxb2.fasta |
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| diff -r 156b60c1530f -r ef2c525bd8cd freebayes.xml --- a/freebayes.xml Wed Oct 25 08:29:45 2017 -0400 +++ b/freebayes.xml Wed Nov 06 17:02:57 2019 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-0">\n+<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@">\n <description>bayesian genetic variant detector</description>\n <macros>\n <import>macros.xml</import>\n@@ -77,26 +77,29 @@\n ## Outputs\n --vcf \'./vcf_output/part_\\$i.vcf\'\n \n+ ## Coverage\n+ #if str($coverage_options.coverage_options_selector) == "set":\n+ @COVERAGE@\n+ #end if\n+\n ##advanced options\n #if str( $options_type.options_type_selector ) == "simple":\n #pass\n #elif str( $options_type.options_type_selector ) == "simple_w_filters":\n --standard-filters\n- --min-coverage ${options_type.min_coverage}\n #elif str( $options_type.options_type_selector ) == "naive":\n --haplotype-length 0\n --min-alternate-count 1\n- --min-alternate-fraction 0\n+ --min-alternate-fraction 0.05\n --pooled-continuous\n --report-monomorphic\n #elif str( $options_type.options_type_selector ) == "naive_w_filters":\n --haplotype-length 0\n --min-alternate-count 1\n- --min-alternate-fraction 0\n+ --min-alternate-fraction 0.05\n --pooled-continuous\n --report-monomorphic\n --standard-filters\n- --min-coverage ${options_type.min_coverage}\n #elif str( $options_type.options_type_selector ) == "full":\n #if str( $options_type.optional_inputs.optional_inputs_selector ) == \'set\':\n ${options_type.optional_inputs.report_monomorphic}\n@@ -189,7 +192,6 @@\n --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}\n #end if\n \n- --min-coverage ${options_type.input_filters.min_coverage}\n --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}\n #end if\n \n@@ -305,6 +307,17 @@\n <param name="region_end" type="integer" label="Region End" value="" />\n </when>\n </conditional>\n+ <conditional name="coverage_options">\n+ <param name="coverage_options_selector" type="select" label="Read coverage"\n+ help="Sets --min-coverage, --limit-coverage, and --skip-coverage">\n+ <option value="do_not_set" selected="true">Use defaults</option>\n+ <option value="set">Specify coverage options</option>\n+ </param>\n+ <when value="set">\n+ <expand macro="par_min_cov" />\n+ </when>\n+ <when value="do_not_set" />\n+ </conditional>\n <conditional name="options_type">\n <param name="options_type_selector" type="select" label="Choose parameter selection level"\n help="Select how much control over the freebayes run you need">\n@@ -315,6 +328,7 @@\n <option value="full">5. Full list of options</option>\n </param>\n <when value="full">\n+\n <conditional name="optional_inputs">\n <param name="optional_inputs_selector" type="select" label="Additional inputs"\n help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">\n@@ -439,7 +453,7 @@\n label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />\n <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"\n label="When assembling observations across repeats, require the total repeat length at least this many bp" />\n- <param name="min_repe'..b' Disable estimation of the probability of the combination\n+ arising under HWE given the allele frequency as estimated\n+ by observation frequency.\n+ --binomial-obs-priors-off Disable incorporation of prior expectations about observations.\n+ Uses read placement probability, strand balance probability,\n+ and read position (5\'-3\') probability.\n+ --allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles\n+ as a component of the priors.\n+\n+**Genotype likelihoods**::\n+\n+ --observation-bias FILE Read length-dependent allele observation biases from FILE.\n+ The format is [length] [alignment efficiency relative to reference]\n+ where the efficiency is 1 if there is no relative observation bias.\n+ --base-quality-cap Q Limit estimated observation quality by capping base quality at Q.\n+ --prob-contamination F An estimate of contamination to use for all samples. default: 10e-9\n+ --legacy-gls Use legacy (polybayes equivalent) genotype likelihood calculations\n+ --contamination-estimates FILE A file containing per-sample estimates of contamination, such as\n+ those generated by VerifyBamID. The format should be:\n+ sample p(read=R|genotype=AR) p(read=A|genotype=AA)\n+ Sample \'*\' can be used to set default contamination estimates.\n+\n+**Algorithmic features**::\n+\n+ --report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided\n+ from genotype likelihoods.\n+ --genotyping-max-iterations N Iterate no more than N times during genotyping step. default: 1000.\n+ --genotyping-max-banddepth N Integrate no deeper than the Nth best genotype by likelihood when\n+ genotyping. default: 6.\n+ --posterior-integration-limits N,M Integrate all genotype combinations in our posterior space\n+ which include no more than N samples with their Mth best\n+ data likelihood. default: 1,3.\n+ --exclude-unobserved-genotypes Skip sample genotypings for which the sample has no supporting reads.\n+ --genotype-variant-threshold N Limit posterior integration to samples where the second-best\n+ genotype likelihood is no more than log(N) from the highest\n+ genotype likelihood for the sample. default: ~unbounded\n+ --use-mapping-quality Use mapping quality of alleles when calculating data likelihoods.\n+ --harmonic-indel-quality Use a weighted sum of base qualities around an indel, scaled by the\n+ distance from the indel. By default use a minimum BQ in flanking sequence.\n+ --read-dependence-factor N Incorporate non-independence of reads by scaling successive\n+ observations by this factor during data likelihood\n+ calculations. default: 0.9\n+ --genotype-qualities Calculate the marginal probability of genotypes and report as GQ in\n+ each sample field in the VCF output.\n+\n+------\n+\n **Acknowledgments**\n \n The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.\n TNG was developed by Bjoern Gruening.\n+]]>\n </help>\n <expand macro="citations">\n <citation type="bibtex">\n' |
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| diff -r 156b60c1530f -r ef2c525bd8cd leftalign.xml --- a/leftalign.xml Wed Oct 25 08:29:45 2017 -0400 +++ b/leftalign.xml Wed Nov 06 17:02:57 2019 -0500 |
| b |
| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="bamleftalign" name="BamLeftAlign" version="@DEPENDENCY_VERSION@-0"> +<tool id="bamleftalign" name="BamLeftAlign" version="@DEPENDENCY_VERSION@"> <description> indels in BAM datasets</description> <macros> <import>macros.xml</import> @@ -40,7 +40,7 @@ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> - <when value="history"> + <when value="history"> <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" argument="--fasta-reference" /> </when> |
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| diff -r 156b60c1530f -r ef2c525bd8cd macros.xml --- a/macros.xml Wed Oct 25 08:29:45 2017 -0400 +++ b/macros.xml Wed Nov 06 17:02:57 2019 -0500 |
| b |
| @@ -1,9 +1,9 @@ <macros> - <token name="@DEPENDENCY_VERSION@">1.1.0.46</token> + <token name="@DEPENDENCY_VERSION@">1.3.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="1.9">samtools</requirement> <yield /> </requirements> </xml> @@ -43,7 +43,14 @@ </when> </conditional> </xml> + <token name="@COVERAGE@"> + --min-coverage ${coverage_options.min_coverage} + --skip-coverage ${coverage_options.skip_coverage} + --limit-coverage ${coverage_options.limit_coverage} + </token> <xml name="par_min_cov"> - <param name="min_coverage" argument="--coverage" type="integer" value="0" label="Require at least this coverage to process a site" /> + <param name="min_coverage" argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" /> + <param name="limit_coverage" argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" /> + <param name="skip_coverage" argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" /> </xml> </macros> |
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| diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-hxb2-test5.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-hxb2-test5.vcf Wed Nov 06 17:02:57 2019 -0500 |
| b |
| b'@@ -0,0 +1,74 @@\n+##fileformat=VCFv4.2\n+##fileDate=20191101\n+##source=freeBayes v1.3.1-dirty\n+##reference=localref.fa\n+##contig=<ID=K03455,length=9719>\n+##phasing=none\n+##commandline="freebayes --region K03455:0..9719 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_K03455:0..9719.vcf --min-coverage 250 --skip-coverage 0 --limit-coverage 0"\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">\n+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">\n+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">\n+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">\n+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">\n+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">\n+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">\n+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">\n+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">\n+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">\n+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">\n+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">\n+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">\n+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">\n+##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">\n+##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">\n+##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">\n+##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">\n+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">\n+##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">\n+##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">\n+##INFO=<ID=RPL,N'..b'33.429;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=927.877;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=23333;QR=0;RO=0;RPL=319;RPP=5.56651;RPPR=0;RPR=347;RUN=1;SAF=474;SAP=262.296;SAR=192;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:666:0,666:0:0:666:23333:-2098.99,-200.486,0\n+K03455\t2802\t.\tC\tA\t3.80909e-14\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=672;DPB=672;DPRA=0;EPP=126.784;EPPR=65.6713;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=627.193;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1084;QR=20184;RO=613;RPL=56;RPP=118.251;RPPR=63.8009;RPR=1;RUN=1;SAF=56;SAP=118.251;SAR=1;SRF=403;SRP=134.96;SRR=210;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:672:613,57:613:20184:57:1084:0,-104.146,-1718.1\n+K03455\t2848\t.\tTAAAAAAGAAAAAATC\tTAAAAAAAGAAAAAATC\t18102\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=630;CIGAR=1M1I15M;DP=722;DPB=774.875;DPRA=0;EPP=43.2136;EPPR=13.8677;GTI=0;LEN=1;MEANALT=40;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=830.486;PAIRED=1;PAIREDR=1;PAO=22;PQA=531.5;PQR=553.5;PRO=23;QA=20369;QR=158;RO=5;RPL=282;RPP=18.0245;RPPR=3.44459;RPR=348;RUN=1;SAF=333;SAP=7.47733;SAR=297;SRF=3;SRP=3.44459;SRR=2;TYPE=ins;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:722:5,630:5:158:630:20369:-1818.16,-176.934,0\n+K03455\t2873\t.\tAC\tAT\t21993.4\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=754;CIGAR=1M1X;DP=773;DPB=775.5;DPRA=0;EPP=5.26817;EPPR=5.18177;GTI=0;LEN=1;MEANALT=5;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1039.03;PAIRED=1;PAIREDR=1;PAO=2.5;PQA=63;PQR=63;PRO=2.5;QA=24534;QR=37;RO=1;RPL=357;RPP=7.6182;RPPR=5.18177;RPR=397;RUN=1;SAF=378;SAP=3.02182;SAR=376;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:773:1,754:1:37:754:24534:-2203.73,-223.941,0\n+K03455\t2882\t.\tG\tT\t21924\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=721;CIGAR=1X;DP=736;DPB=736;DPRA=0;EPP=36.2149;EPPR=22.5536;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=945.018;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24583;QR=177;RO=9;RPL=353;RPP=3.68794;RPPR=9.04217;RPR=368;RUN=1;SAF=363;SAP=3.08559;SAR=358;SRF=7;SRP=9.04217;SRR=2;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:736:9,721:9:177:721:24583:-2195.37,-203.838,0\n+K03455\t2883\t.\tGGT\tGGG\t2.65192e-14\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=46;CIGAR=2M1X;DP=726;DPB=731;DPRA=0;EPP=86.2815;EPPR=8.74455;GTI=0;LEN=1;MEANALT=6;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=660.068;PAIRED=1;PAIREDR=1;PAO=3.5;PQA=112;PQR=112;PRO=4.5;QA=1167;QR=22483;RO=668;RPL=43;RPP=78.5398;RPPR=3.12733;RPR=3;RUN=1;SAF=45;SAP=94.401;SAR=1;SRF=316;SRP=7.22322;SRR=352;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:726:668,46:668:22483:46:1167:0,-109.931,-1917.55\n+K03455\t2894\t.\tT\tC\t21733.9\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=717;CIGAR=1X;DP=723;DPB=723;DPRA=0;EPP=10.8876;EPPR=5.18177;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=991.951;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24231;QR=17;RO=1;RPL=373;RPP=5.55731;RPPR=5.18177;RPR=344;RUN=1;SAF=354;SAP=3.25561;SAR=363;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:723:1,717:1:17:717:24231:-2178.13,-214.613,0\n+K03455\t2906\t.\tC\tT\t20694.7\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=650;CIGAR=1X;DP=653;DPB=653;DPRA=0;EPP=3.86553;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=885.229;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23147;QR=65;RO=2;RPL=368;RPP=27.7183;RPPR=7.35324;RPR=282;RUN=1;SAF=301;SAP=10.7073;SAR=349;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:653:2,650:2:65:650:23147:-2076.11,-190.301,0\n+K03455\t2913\t.\tG\tA\t20816.6\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=638;CIGAR=1X;DP=639;DPB=639;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=878.93;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23329;QR=31;RO=1;RPL=402;RPP=96.7988;RPPR=5.18177;RPR=236;RUN=1;SAF=297;SAP=9.5996;SAR=341;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:639:1,638:1:31:638:23329:-2095.39,-189.259,0\n' |
| b |
| diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-hxb2-test6.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-hxb2-test6.vcf Wed Nov 06 17:02:57 2019 -0500 |
| b |
| b'@@ -0,0 +1,83 @@\n+##fileformat=VCFv4.2\n+##fileDate=20191106\n+##source=freeBayes v1.3.1-dirty\n+##reference=localref.fa\n+##contig=<ID=K03455,length=9719>\n+##phasing=none\n+##commandline="freebayes --region K03455:0..9719 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_K03455:0..9719.vcf --min-coverage 0 --skip-coverage 0 --limit-coverage 400"\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">\n+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">\n+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">\n+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">\n+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">\n+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">\n+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">\n+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">\n+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">\n+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">\n+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">\n+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">\n+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">\n+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">\n+##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">\n+##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">\n+##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">\n+##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">\n+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">\n+##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">\n+##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">\n+##INFO=<ID=RPL,N'..b'GT:DP:AD:RO:QR:AO:QA:GL\t1/1:723:1,717:1:17:717:24231:-2178.13,-214.613,0\n+K03455\t2906\t.\tC\tT\t20694.7\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=650;CIGAR=1X;DP=653;DPB=653;DPRA=0;EPP=3.86553;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=885.229;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23147;QR=65;RO=2;RPL=368;RPP=27.7183;RPPR=7.35324;RPR=282;RUN=1;SAF=301;SAP=10.7073;SAR=349;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:653:2,650:2:65:650:23147:-2076.11,-190.301,0\n+K03455\t2913\t.\tG\tA\t20816.6\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=638;CIGAR=1X;DP=639;DPB=639;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=878.93;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23329;QR=31;RO=1;RPL=402;RPP=96.7988;RPPR=5.18177;RPR=236;RUN=1;SAF=297;SAP=9.5996;SAR=341;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:639:1,638:1:31:638:23329:-2095.39,-189.259,0\n+K03455\t2987\t.\tC\tT\t6415.71\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=234;CIGAR=1X;DP=235;DPB=235;DPRA=0;EPP=16.4103;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=328.998;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7972;QR=0;RO=0;RPL=234;RPP=511.135;RPPR=0;RPR=0;RUN=1;SAF=98;SAP=16.4103;SAR=136;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:235:0,234:0:0:234:7972:-717.259,-70.441,0\n+K03455\t2992\t.\tT\tG\t2.14568e-14\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=1X;DP=202;DPB=202;DPRA=0;EPP=26.8965;EPPR=8.54184;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=220.335;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=218;QR=6192;RO=190;RPL=11;RPP=26.8965;RPPR=415.59;RPR=0;RUN=1;SAF=11;SAP=26.8965;SAR=0;SRF=84;SRP=8.54184;SRR=106;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:202:190,11:190:6192:11:218:0,-40.8623,-537.516\n+K03455\t3016\t.\tCACCA\tCACCG\t2027.61\t.\tAB=0;ABP=0;AC=2;AF=1;AN=2;AO=81;CIGAR=4M1X;DP=92;DPB=92.4;DPRA=0;EPP=25.5561;EPPR=0;GTI=0;LEN=1;MEANALT=6;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=86.0691;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2598;QR=0;RO=0;RPL=81;RPP=178.9;RPPR=0;RPR=0;RUN=1;SAF=55;SAP=25.5561;SAR=26;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t1/1:92:0,81:0:0:81:2598:-233.803,-24.3834,0\n+K03455\t3025\t.\tT\tA\t0\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=9.52472;EPPR=4.6389;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.9298;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1423;RO=48;RPL=3;RPP=9.52472;RPPR=107.241;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=27;SRP=4.6389;SRR=21;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:51:48,3:48:1423:3:45:0,-11.1526,-124.109\n+K03455\t3035\t.\tT\tA\t2.21948e-14\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=9.52472;EPPR=4.65535;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.669;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=54;QR=954;RO=33;RPL=3;RPP=9.52472;RPPR=74.6689;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=19;SRP=4.65535;SRR=14;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:37:33,3:33:954:3:54:0,-5.96965,-81.0818\n+K03455\t3036\t.\tA\tG\t1.09205e-09\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=9.52472;EPPR=26.2761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.1038;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=578;RO=21;RPL=3;RPP=9.52472;RPPR=48.6112;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=18;SRP=26.2761;SRR=3;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:24:21,3:21:578:3:67:0,-0.971771,-46.0254\n+K03455\t3042\t.\tA\tC\t7.93379e-05\t.\tAB=0.25;ABP=9.52472;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=9.52472;EPPR=14.8328;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.9103;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=52;QR=233;RO=9;RPL=3;RPP=9.52472;RPPR=22.5536;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=8;SRP=14.8328;SRR=1;TYPE=snp;technology.ILLUMINA=1\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:12:9,3:9:233:3:52:-1.24091,0,-17.6087\n' |
| b |
| diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-hxb2-test7.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-hxb2-test7.vcf Wed Nov 06 17:02:57 2019 -0500 |
| b |
| @@ -0,0 +1,62 @@ +##fileformat=VCFv4.2 +##fileDate=20191030 +##source=freeBayes v1.3.1-dirty +##reference=localref.fa +##contig=<ID=K03455,length=9719> +##phasing=none +##commandline="freebayes --region K03455:0..9719 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_K03455:0..9719.vcf --min-coverage 0 --skip-coverage 100 --limit-coverage 0" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##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"> +##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"> +##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"> +##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"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##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"> +##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"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##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"> +##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"> +##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."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##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."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> +##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##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"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 |
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| diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-hxb2.bam |
| b |
| Binary file test-data/freebayes-hxb2.bam has changed |
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| diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-hxb2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-hxb2.fasta Wed Nov 06 17:02:57 2019 -0500 |
| b |
| b'@@ -0,0 +1,2 @@\n+>K03455\n+TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCA'..b'CAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA\n' |
| b |
| diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-phix174-test1.vcf --- a/test-data/freebayes-phix174-test1.vcf Wed Oct 25 08:29:45 2017 -0400 +++ b/test-data/freebayes-phix174-test1.vcf Wed Nov 06 17:02:57 2019 -0500 |
| b |
| b'@@ -1,4 +1,6 @@\n ##fileformat=VCFv4.2\n+##fileDate=20191030\n+##source=freeBayes v1.3.1-dirty\n ##reference=localref.fa\n ##contig=<ID=phiX174,length=5386>\n ##phasing=none\n@@ -66,7 +68,9 @@\n phiX174\t1445\t.\tC\tA\t0.147157\t.\tAB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=3.36782;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPL=1;RPP=3.0103;RPPR=6.91895;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:7:5,2:5:273:2:76:-2.52649,0,-12.4911\n phiX174\t1577\t.\tA\tC\t0.0123232\t.\tAB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=5.8634;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPL=1;RPP=3.0103;RPPR=10.7656;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:9:7,2:7:460:2:60:-1.81064,0,-19.8257\n phiX174\t1631\t.\tT\tG\t0.00100612\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=8.3701;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:10:8,2:8:500:2:68:-1.52818,0,-17.3788\n+phiX174\t1665\t.\tC\tA\t0.0164128\t.\tAB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=37;MQMR=30.3333;NS=1;NUMALT=1;ODDS=5.57635;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=587;RO=9;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:12:9,2:9:587:2:65:-2.35331,0,-21.269\n phiX174\t1772\t.\tT\tG\t0.0180574\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=5.48067;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:10:7,2:7:425:2:59:-1.97686,0,-17.3816\n+phiX174\t1786\t.\tT\tG\t7.94817e-05\t.\tAB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.9085;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=537;RO=10;RPL=0;RPP=7.35324;RPPR=6.48466;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=16.9077;SRR=9;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:12:10,2:10:537:2:59:-0.861483,0,-25.1364\n phiX174\t1945\t.\tT\tG\t1.01422\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=1.3354;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:6:4,2:4:263:2:59:-3.25425,0,-11.8637\n phiX174\t2230\t.\tT\tG\t0.00580188\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=35.5;NS=1;NUMALT=1;ODDS=6.61746;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=491;RO=8;RPL=0;RPP=7.35324;RPPR=4.09604;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:10:8,2:8:491:2:80:-2.28934,0,-22.3591\n phiX174\t2699\t.\tC\tA\t2.04855\t.\tAB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=0.517362;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=109;RO=2;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:4:2,2:2:109:2:76:-3.4054,0,-5.58455\n@@ -76,10 +80,14 @@\n phiX174\t2983\t.\t'..b'IREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:6:4,2:4:284:2:58:-2.65031,0,-9.66348\n+phiX174\t3413\t.\tT\tG\t0.00284067\t.\tAB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31.6667;NS=1;NUMALT=1;ODDS=7.33194;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=537;RO=9;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=14.8328;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:11:9,2:9:537:2:57:-1.59087,0,-22.4183\n phiX174\t3418\t.\tA\tC\t0.000937887\t.\tAB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=8.44033;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPL=2;RPP=7.35324;RPPR=4.09604;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:10:8,2:8:526:2:60:-1.49768,0,-21.0207\n+phiX174\t3490\t.\tA\tC\t0.00226584\t.\tAB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=7.35324;EPPR=9.04217;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34.3333;NS=1;NUMALT=1;ODDS=7.5581;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=543;RO=9;RPL=2;RPP=7.35324;RPPR=9.04217;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:11:9,2:9:543:2:66:-2.09471,0,-24.3433\n phiX174\t3729\t.\tC\tT\t0.295112\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=2.65478;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=232;RO=4;RPL=2;RPP=7.35324;RPPR=5.18177;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:6:4,2:4:232:2:63:-3.28331,0,-11.7007\n phiX174\t4031\t.\tT\tG\t0.0784807\t.\tAB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=4.00441;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:8:6,2:6:322:2:85:-3.02817,0,-11.6802\n phiX174\t4502\t.\tA\tC\t0.232919\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=2.89868;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPL=1;RPP=3.0103;RPPR=11.6962;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:6:4,2:4:284:2:55:-2.57533,0,-11.8832\n phiX174\t4558\t.\tC\tG\t0.076247\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=4.03372;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:6:4,2:4:204:2:59:-2.68445,0,-8.4362\n phiX174\t4655\t.\tT\tG\t0.399408\t.\tAB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=2.33999;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:6:4,2:4:193:2:70:-2.81796,0,-11.1489\n+phiX174\t4704\t.\tT\tC\t0.000171782\t.\tAB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=10.8276;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.1378;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=621;RO=10;RPL=0;RPP=7.35324;RPPR=3.87889;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=3.87889;SRR=6;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:12:10,2:10:621:2:58:-1.1962,0,-26.2058\n' |
| b |
| diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-phix174-test2.vcf --- a/test-data/freebayes-phix174-test2.vcf Wed Oct 25 08:29:45 2017 -0400 +++ b/test-data/freebayes-phix174-test2.vcf Wed Nov 06 17:02:57 2019 -0500 |
| b |
| @@ -1,8 +1,10 @@ ##fileformat=VCFv4.2 +##fileDate=20191031 +##source=freeBayes v1.3.1-dirty ##reference=localref.fa ##contig=<ID=phiX174,length=5386> ##phasing=none -##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" +##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" ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> |
| b |
| diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-phix174-test3.vcf --- a/test-data/freebayes-phix174-test3.vcf Wed Oct 25 08:29:45 2017 -0400 +++ b/test-data/freebayes-phix174-test3.vcf Wed Nov 06 17:02:57 2019 -0500 |
| b |
| @@ -1,8 +1,10 @@ ##fileformat=VCFv4.2 +##fileDate=20191031 +##source=freeBayes v1.3.1-dirty ##reference=localref.fa ##contig=<ID=phiX174,length=5386> ##phasing=none -##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" +##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" ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> |
| b |
| diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-phix174-test4.vcf --- a/test-data/freebayes-phix174-test4.vcf Wed Oct 25 08:29:45 2017 -0400 +++ b/test-data/freebayes-phix174-test4.vcf Wed Nov 06 17:02:57 2019 -0500 |
| b |
| b'@@ -1,4 +1,6 @@\n ##fileformat=VCFv4.2\n+##fileDate=20191030\n+##source=freeBayes v1.3.1-dirty\n ##reference=localref.fa\n ##contig=<ID=phiX174,length=5386>\n ##phasing=none\n@@ -66,7 +68,9 @@\n phiX174\t1445\t.\tC\tA\t3.85961e-09\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=20.8413;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPL=1;RPP=3.0103;RPPR=6.91895;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:7:5,2:5:273:2:76:0,-9.96463\n phiX174\t1577\t.\tA\tC\t7.60962e-15\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=38.7543;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPL=1;RPP=3.0103;RPPR=10.7656;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:9:7,2:7:460:2:60:0,-18.0151\n phiX174\t1631\t.\tT\tG\t8.14828e-15\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=36.3199;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:10:8,2:8:500:2:68:0,-15.8506\n+phiX174\t1665\t.\tC\tA\t1.45784e-14\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=37;MQMR=30.3333;NS=1;NUMALT=1;ODDS=41.3105;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=587;RO=9;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:12:9,2:9:587:2:65:0,-18.9157\n phiX174\t1772\t.\tT\tG\t2.89903e-14\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=32.7439;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:10:7,2:7:425:2:59:0,-15.4048\n+phiX174\t1786\t.\tT\tG\t0\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.4;NS=1;NUMALT=1;ODDS=51.6968;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=537;RO=10;RPL=0;RPP=7.35324;RPPR=6.48466;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=16.9077;SRR=9;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:12:10,2:10:537:2:59:0,-24.2749\n phiX174\t1945\t.\tT\tG\t2.84647e-08\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=18.8432;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:6:4,2:4:263:2:59:0,-8.60945\n phiX174\t2230\t.\tT\tG\t1.46203e-15\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=35.5;NS=1;NUMALT=1;ODDS=46.0348;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=491;RO=8;RPL=0;RPP=7.35324;RPPR=4.09604;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:10:8,2:8:491:2:80:0,-20.0697\n phiX174\t2699\t.\tC\tA\t0.0286554\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=5.01766;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=109;RO=2;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:4:2,2:2:109:2:76:0,-2.17914\n@@ -76,10 +80,14 @@\n phiX174\t2983\t.\tT\tG\t0.000276493\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33;NS=1;NUMALT=1;ODDS=9.66185;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PR'..b'O:QR:AO:QA:GL\t0:13:11,2:11:738:2:75:0,-29.1064\n phiX174\t3325\t.\tA\tC\t2.80881e-07\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=31;NS=1;NUMALT=1;ODDS=16.5539;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:6:4,2:4:284:2:58:0,-7.01317\n+phiX174\t3413\t.\tT\tG\t6.16289e-15\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31.6667;NS=1;NUMALT=1;ODDS=43.4788;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=537;RO=9;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=14.8328;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:11:9,2:9:537:2:57:0,-20.8274\n phiX174\t3418\t.\tA\tC\t0\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=44.7759;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPL=2;RPP=7.35324;RPPR=4.09604;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:10:8,2:8:526:2:60:0,-19.523\n+phiX174\t3490\t.\tA\tC\t0\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=7.35324;EPPR=9.04217;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34.3333;NS=1;NUMALT=1;ODDS=43.8402;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=543;RO=9;RPL=2;RPP=7.35324;RPPR=9.04217;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:11:9,2:9:543:2:66:0,-22.2486\n phiX174\t3729\t.\tC\tT\t6.64464e-08\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=17.9954;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=232;RO=4;RPL=2;RPP=7.35324;RPPR=5.18177;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:6:4,2:4:232:2:63:0,-8.41737\n phiX174\t4031\t.\tT\tG\t2.20192e-08\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=19.0999;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:8:6,2:6:322:2:85:0,-8.65207\n phiX174\t4502\t.\tA\tC\t3.4202e-08\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=18.6595;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPL=1;RPP=3.0103;RPPR=11.6962;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:6:4,2:4:284:2:55:0,-9.30785\n phiX174\t4558\t.\tC\tG\t1.36745e-05\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=12.6685;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:6:4,2:4:204:2:59:0,-5.75175\n phiX174\t4655\t.\tT\tG\t1.44134e-07\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=17.2211;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:6:4,2:4:193:2:70:0,-8.33095\n+phiX174\t4704\t.\tT\tC\t1.08534e-15\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=10.8276;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33.4;NS=1;NUMALT=1;ODDS=55.4522;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=621;RO=10;RPL=0;RPP=7.35324;RPPR=3.87889;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=3.87889;SRR=6;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:12:10,2:10:621:2:58:0,-25.0096\n' |