| Previous changeset 26:a028d13cd860 (2017-05-04) Next changeset 28:977a5301b66d (2017-06-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870 |
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modified:
freebayes.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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| diff -r a028d13cd860 -r 9f164587a92f freebayes.xml --- a/freebayes.xml Thu May 04 11:34:13 2017 -0400 +++ b/freebayes.xml Tue Jun 06 11:44:38 2017 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-3"> +<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-0"> <description>bayesian genetic variant detector</description> <macros> <import>macros.xml</import> @@ -24,7 +24,13 @@ #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if - #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): + #if $reference_source.batchmode.processmode == 'merge': + #set $input_bamfiles = $reference_source.batchmode.input_bams + #else: + #set $input_bamfiles = [ $reference_source.batchmode.input_bams ] + #end if + + #for $bam_count, $input_bam in enumerate( $input_bamfiles ): ln -s -f '${input_bam}' 'b_${bam_count}.bam' && ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' && #end for @@ -43,7 +49,7 @@ printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed && #else ##divide up the regions in the bam file for efficient processing - #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): + #for $bam_count, $input_bam in enumerate( $input_bamfiles ): samtools view -H b_${bam_count}.bam | grep "^@SQ" | cut -f 2- | @@ -53,8 +59,6 @@ #end for #end if - - sort -u regions_all.bed > regions_uniq.bed && ## split into even small chunks, this has some disatvantages and will not be used for the moment ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed && @@ -76,7 +80,7 @@ --region '\$i' - #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): + #for $bam_count, $input_bam in enumerate( $input_bamfiles ): --bam 'b_${bam_count}.bam' #end for --fasta-reference '${reference_fasta_filename}' @@ -283,17 +287,16 @@ <option value="history">History</option> </param> <when value="cached"> - <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> - </param> + <expand macro="input_bam"> + <expand macro="validation" /> + </expand> <param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="fasta_indexes"></options> + <options from_data_table="fasta_indexes" /> <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"> <!-- FIX ME!!!! --> - <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file" /> + <expand macro="input_bam" /> <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> </when> @@ -646,6 +649,7 @@ <tests> <test> <param name="reference_source_selector" value="history" /> + <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/> <param name="options_type_selector" value="simple"/> @@ -653,6 +657,7 @@ </test> <test> <param name="reference_source_selector" value="history" /> + <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/> <param name="options_type_selector" value="naive_w_filters"/> @@ -661,6 +666,7 @@ </test> <test> <param name="reference_source_selector" value="history" /> + <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/> <param name="options_type_selector" value="naive_w_filters"/> @@ -669,6 +675,7 @@ </test> <test> <param name="reference_source_selector" value="history" /> + <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/> <param name="options_type_selector" value="full"/> |
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| diff -r a028d13cd860 -r 9f164587a92f macros.xml --- a/macros.xml Thu May 04 11:34:13 2017 -0400 +++ b/macros.xml Tue Jun 06 11:44:38 2017 -0400 |
| b |
| @@ -1,20 +1,41 @@ <macros> - <token name="@DEPENDENCY_VERSION@">1.0.2.29</token> + <token name="@DEPENDENCY_VERSION@">1.1.0</token> <xml name="citations"> <citations> <citation type="bibtex"> - @misc{1207.3907, - Author = {Erik Garrison}, - Title = {Haplotype-based variant detection from short-read sequencing}, - Year = {2012}, - Eprint = {arXiv:1207.3907}, - url = {http://arxiv.org/abs/1207.3907} - } + @misc{1207.3907, + Author = {Erik Garrison}, + Title = {Haplotype-based variant detection from short-read sequencing}, + Year = {2012}, + Eprint = {arXiv:1207.3907}, + url = {http://arxiv.org/abs/1207.3907} + } </citation> </citations> </xml> - + <xml name="validation"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + </xml> + <xml name="input_bam"> + <conditional name="batchmode"> + <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF file for each input BAM file. Selecting the merge option will produce one VCF file for all input BAM files." display="radio"> + <option value="individual" selected="True">Run individually</option> + <option value="merge">Merge output VCFs</option> + </param> + <when value="individual"> + <param name="input_bams" type="data" format="bam" label="BAM file"> + <yield /> + </param> + </when> + <when value="merge"> + <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file"> + <yield /> + </param> + </when> + </conditional> + </xml> <xml name="par_min_cov"> <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="default=0" argument="--coverage" /> |
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| diff -r a028d13cd860 -r 9f164587a92f test-data/freebayes-phix174-test1.vcf --- a/test-data/freebayes-phix174-test1.vcf Thu May 04 11:34:13 2017 -0400 +++ b/test-data/freebayes-phix174-test1.vcf Tue Jun 06 11:44:38 2017 -0400 |
| b |
| b'@@ -1,4 +1,4 @@\n-##fileformat=VCFv4.1\n+##fileformat=VCFv4.2\n ##reference=localref.fa\n ##contig=<ID=phiX174,length=5386>\n ##phasing=none\n@@ -9,8 +9,8 @@\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="Reference allele observation count, with partial observations recorded fractionally">\n-##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">\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@@ -50,36 +50,36 @@\n ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">\n ##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">\n ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">\n-##FORMAT=<ID=DPR,Number=A,Type=Integer,Description="Number of observation for each allele">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">\n ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">\n ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">\n ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">\n ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">\n ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">\n #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tunknown\n-phiX174\t311\t.\tA\tG\t0.00392026\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=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.5714;NS=1;NUMALT=1;ODDS=7.0097;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPL=0;RPP=7.35324;RPPR=3.32051;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/1:9:9,2:7:478:2:70:-1.91487,0,-18.7749\n-phiX174\t374\t.\tT\tG\t23.3387\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=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=25;NS=1;NUMALT=1;ODDS=1.58025;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPL=1;RPP=3.0103;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/1:4:4,2:2:141:2:75:-5.19433,0,-3.54586\n-phiX174\t913\t.\tA\tC\t1.83104\t.\tAB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;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=29;NS=1;NUMALT=1;ODDS=0.651489;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=171;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/1:5:5,2:3:171:2:58:-3.42633,0,-6.47921\n-phiX174\t1205\t.\tA\tC\t0.00388031\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=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34;NS=1;NUMALT=1;ODDS=7.01995;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=456;RO=8;RPL=2;RPP=7.35324;RPPR=7.3532'..b'T=1;ODDS=0.843116;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:5:3,2:3:150:2:57:-3.34311,0,-7.61298\n+phiX174\t3110\t.\tT\tC\t1.16857\t.\tAB=0.333333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.73412;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35;NS=1;NUMALT=1;ODDS=1.17522;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=361;RO=6;RPL=0;RPP=9.52472;RPPR=3.0103;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:9:6,3:6:361:3:94:-4.02963,0,-16.4039\n+phiX174\t3155\t.\tT\tG\t5.42491\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=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=0.911202;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPL=1;RPP=3.0103;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/1:7:5,2:5:299:2:75:-4.38484,0,-11.5688\n+phiX174\t3325\t.\tA\tC\t0.0705175\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=25;MQMR=31;NS=1;NUMALT=1;ODDS=4.11232;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\t0/1:6:4,2:4:284:2:58:-2.65031,0,-9.66348\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\t3729\t.\tC\tT\t0.274997\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=2.72772;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;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\t0/1:6:4,2:4:232:2:61:-3.25163,0,-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' |
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| diff -r a028d13cd860 -r 9f164587a92f test-data/freebayes-phix174-test2.vcf --- a/test-data/freebayes-phix174-test2.vcf Thu May 04 11:34:13 2017 -0400 +++ b/test-data/freebayes-phix174-test2.vcf Tue Jun 06 11:44:38 2017 -0400 |
| b |
| b'@@ -1,4 +1,4 @@\n-##fileformat=VCFv4.1\n+##fileformat=VCFv4.2\n ##reference=localref.fa\n ##contig=<ID=phiX174,length=5386>\n ##phasing=none\n@@ -9,8 +9,8 @@\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="Reference allele observation count, with partial observations recorded fractionally">\n-##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">\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@@ -50,29 +50,29 @@\n ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">\n ##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">\n ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">\n-##FORMAT=<ID=DPR,Number=A,Type=Integer,Description="Number of observation for each allele">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">\n ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">\n ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">\n ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">\n ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">\n ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">\n #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tunknown\n-phiX174\t1134\t.\tA\t.\t0\t.\tDP=14;DPB=14;EPPR=3.0103;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=916;RO=14;RPPR=8.59409\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:916:.:.:0\n-phiX174\t1135\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=957;RO=14;RPPR=5.49198\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:957:.:.:0\n-phiX174\t1136\t.\tG\t.\t0\t.\tDP=14;DPB=14;EPPR=8.59409;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=919;RO=14;RPPR=3.0103\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:919:.:.:0\n-phiX174\t1137\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=5.49198;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=14;RPPR=3.63072\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:927:.:.:0\n-phiX174\t1138\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=876;RO=14;RPPR=5.49198\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:876:.:.:0\n-phiX174\t1139\t.\tG\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=946;RO=14;RPPR=5.49198\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:946:.:.:0\n-phiX174\t1140\t.\tT\t.\t0\t.\tDP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=15;RPPR=4.31318\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:15:15:15:927:.:.:0\n-phiX174\t1141\t.\tT\tG\t3.61953e-07\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=16.3003;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=880;RO=14;RPL=0;RPP=5.18177;R'..b'AD:RO:QR:AO:QA:GL\t0/0:14:14:14:916:.:.:0\n+phiX174\t1135\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=957;RO=14;RPPR=5.49198\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:14:14:957:.:.:0\n+phiX174\t1136\t.\tG\t.\t0\t.\tDP=14;DPB=14;EPPR=8.59409;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=919;RO=14;RPPR=3.0103\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:14:14:919:.:.:0\n+phiX174\t1137\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=5.49198;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=14;RPPR=3.63072\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:14:14:927:.:.:0\n+phiX174\t1138\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=876;RO=14;RPPR=5.49198\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:14:14:876:.:.:0\n+phiX174\t1139\t.\tG\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=946;RO=14;RPPR=5.49198\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:14:14:946:.:.:0\n+phiX174\t1140\t.\tT\t.\t0\t.\tDP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=15;RPPR=4.31318\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:927:.:.:0\n+phiX174\t1141\t.\tT\tG\t3.61953e-07\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=16.3003;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=880;RO=14;RPL=0;RPP=5.18177;RPPR=5.49198;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=5.49198;SRR=9;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:14,1:14:880:1:50:0,-0.836684,-42.5367\n+phiX174\t1142\t.\tG\t.\t0\t.\tDP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1082;RO=16;RPPR=3.55317\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:16:16:16:1082:.:.:0\n+phiX174\t1143\t.\tG\t.\t0\t.\tDP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1029;RO=16;RPPR=3.55317\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:16:16:16:1029:.:.:0\n+phiX174\t1144\t.\tC\t.\t0\t.\tDP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1114;RO=16;RPPR=3.55317\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:16:16:16:1114:.:.:0\n+phiX174\t1145\t.\tG\t.\t0\t.\tDP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1042;RO=15;RPPR=3.15506\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:1042:.:.:0\n+phiX174\t1146\t.\tC\t.\t0\t.\tDP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1058;RO=15;RPPR=3.15506\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:1058:.:.:0\n+phiX174\t1147\t.\tT\t.\t0\t.\tDP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=999;RO=15;RPPR=4.31318\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:999:.:.:0\n+phiX174\t1148\t.\tC\t.\t0\t.\tDP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1003;RO=15;RPPR=4.31318\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:1003:.:.:0\n+phiX174\t1149\t.\tT\tC\t4.04114e-07\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=16.1901;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=830;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=4.51363;SRR=8;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:13,1:13:830:1:33:0,-1.0599,-39.8344\n+phiX174\t1151\t.\tC\tT\t3.45599e-08\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=18.6491;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=946;RO=14;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=12.937;SRR=11;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:14,1:14:946:1:27:0,-1.85676,-43.833\n+phiX174\t1152\t.\tG\t.\t0\t.\tDP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=993;RO=16;RPPR=5.18177\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:16:16:16:993:.:.:0\n+phiX174\t1153\t.\tT\t.\t3.38668e-15\t.\tDP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=880;RO=15;RPPR=4.31318\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:880:.:.:0\n' |
| b |
| diff -r a028d13cd860 -r 9f164587a92f test-data/freebayes-phix174-test3.vcf --- a/test-data/freebayes-phix174-test3.vcf Thu May 04 11:34:13 2017 -0400 +++ b/test-data/freebayes-phix174-test3.vcf Tue Jun 06 11:44:38 2017 -0400 |
| b |
| b'@@ -1,4 +1,4 @@\n-##fileformat=VCFv4.1\n+##fileformat=VCFv4.2\n ##reference=localref.fa\n ##contig=<ID=phiX174,length=5386>\n ##phasing=none\n@@ -9,8 +9,8 @@\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="Reference allele observation count, with partial observations recorded fractionally">\n-##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">\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@@ -50,29 +50,29 @@\n ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">\n ##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">\n ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">\n-##FORMAT=<ID=DPR,Number=A,Type=Integer,Description="Number of observation for each allele">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">\n ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">\n ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">\n ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">\n ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">\n ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">\n #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tunknown\n-phiX174\t1134\t.\tA\t.\t0\t.\tDP=14;DPB=14;EPPR=3.0103;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=916;RO=14;RPPR=8.59409\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:916:.:.:0\n-phiX174\t1135\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=957;RO=14;RPPR=5.49198\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:957:.:.:0\n-phiX174\t1136\t.\tG\t.\t0\t.\tDP=14;DPB=14;EPPR=8.59409;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=919;RO=14;RPPR=3.0103\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:919:.:.:0\n-phiX174\t1137\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=5.49198;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=14;RPPR=3.63072\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:927:.:.:0\n-phiX174\t1138\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=876;RO=14;RPPR=5.49198\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:876:.:.:0\n-phiX174\t1139\t.\tG\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=946;RO=14;RPPR=5.49198\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:14:14:14:946:.:.:0\n-phiX174\t1140\t.\tT\t.\t0\t.\tDP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=15;RPPR=4.31318\tGT:DP:DPR:RO:QR:AO:QA:GL\t0/0:15:15:15:927:.:.:0\n-phiX174\t1141\t.\tT\tG\t3.61953e-07\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=16.3003;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=880;RO=14;RPL=0;RPP=5.18177;R'..b'AD:RO:QR:AO:QA:GL\t0/0:14:14:14:916:.:.:0\n+phiX174\t1135\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=957;RO=14;RPPR=5.49198\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:14:14:957:.:.:0\n+phiX174\t1136\t.\tG\t.\t0\t.\tDP=14;DPB=14;EPPR=8.59409;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=919;RO=14;RPPR=3.0103\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:14:14:919:.:.:0\n+phiX174\t1137\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=5.49198;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=14;RPPR=3.63072\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:14:14:927:.:.:0\n+phiX174\t1138\t.\tC\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=876;RO=14;RPPR=5.49198\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:14:14:876:.:.:0\n+phiX174\t1139\t.\tG\t.\t0\t.\tDP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=946;RO=14;RPPR=5.49198\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:14:14:946:.:.:0\n+phiX174\t1140\t.\tT\t.\t0\t.\tDP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=15;RPPR=4.31318\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:927:.:.:0\n+phiX174\t1141\t.\tT\tG\t3.61953e-07\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=16.3003;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=880;RO=14;RPL=0;RPP=5.18177;RPPR=5.49198;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=5.49198;SRR=9;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:14,1:14:880:1:50:0,-0.836684,-42.5367\n+phiX174\t1142\t.\tG\t.\t0\t.\tDP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1082;RO=16;RPPR=3.55317\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:16:16:16:1082:.:.:0\n+phiX174\t1143\t.\tG\t.\t0\t.\tDP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1029;RO=16;RPPR=3.55317\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:16:16:16:1029:.:.:0\n+phiX174\t1144\t.\tC\t.\t0\t.\tDP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1114;RO=16;RPPR=3.55317\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:16:16:16:1114:.:.:0\n+phiX174\t1145\t.\tG\t.\t0\t.\tDP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1042;RO=15;RPPR=3.15506\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:1042:.:.:0\n+phiX174\t1146\t.\tC\t.\t0\t.\tDP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1058;RO=15;RPPR=3.15506\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:1058:.:.:0\n+phiX174\t1147\t.\tT\t.\t0\t.\tDP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=999;RO=15;RPPR=4.31318\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:999:.:.:0\n+phiX174\t1148\t.\tC\t.\t0\t.\tDP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1003;RO=15;RPPR=4.31318\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:1003:.:.:0\n+phiX174\t1149\t.\tT\tC\t4.04114e-07\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=16.1901;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=830;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=4.51363;SRR=8;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:14:13,1:13:830:1:33:0,-1.0599,-39.8344\n+phiX174\t1151\t.\tC\tT\t3.45599e-08\t.\tAB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=18.6491;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=946;RO=14;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=12.937;SRR=11;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:14,1:14:946:1:27:0,-1.85676,-43.833\n+phiX174\t1152\t.\tG\t.\t0\t.\tDP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=993;RO=16;RPPR=5.18177\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:16:16:16:993:.:.:0\n+phiX174\t1153\t.\tT\t.\t3.38668e-15\t.\tDP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=880;RO=15;RPPR=4.31318\tGT:DP:AD:RO:QR:AO:QA:GL\t0/0:15:15:15:880:.:.:0\n' |
| b |
| diff -r a028d13cd860 -r 9f164587a92f test-data/freebayes-phix174-test4.vcf --- a/test-data/freebayes-phix174-test4.vcf Thu May 04 11:34:13 2017 -0400 +++ b/test-data/freebayes-phix174-test4.vcf Tue Jun 06 11:44:38 2017 -0400 |
| b |
| b'@@ -1,4 +1,4 @@\n-##fileformat=VCFv4.1\n+##fileformat=VCFv4.2\n ##reference=localref.fa\n ##contig=<ID=phiX174,length=5386>\n ##phasing=none\n@@ -9,8 +9,8 @@\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="Reference allele observation count, with partial observations recorded fractionally">\n-##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">\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@@ -50,35 +50,35 @@\n ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">\n ##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">\n ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">\n-##FORMAT=<ID=DPR,Number=A,Type=Integer,Description="Number of observation for each allele">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">\n ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">\n ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">\n ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">\n ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">\n ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">\n #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tunknown\n-phiX174\t311\t.\tA\tG\t5.72946e-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=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.5714;NS=1;NUMALT=1;ODDS=38.0687;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPL=0;RPP=7.35324;RPPR=3.32051;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp\tGT:DP:DPR:RO:QR:AO:QA:GL\t0:9:9,2:7:478:2:70:0,-16.86\n-phiX174\t374\t.\tT\tG\t22.5297\t.\tAB=0;ABP=0;AC=1;AF=1;AN=1;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=25;NS=1;NUMALT=1;ODDS=5.18205;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPL=1;RPP=3.0103;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp\tGT:DP:DPR:RO:QR:AO:QA:GL\t1:4:4,2:2:141:2:75:-1.64847,0\n-phiX174\t913\t.\tA\tC\t0.0136501\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=29;NS=1;NUMALT=1;ODDS=5.76099;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=171;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp\tGT:DP:DPR:RO:QR:AO:QA:GL\t0:5:5,2:3:171:2:58:0,-3.05287\n-phiX174\t1205\t.\tA\tC\t6.98431e-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=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34;NS=1;NUMALT=1;ODDS=41.7843;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=456;RO=8;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=7.35324;SRR=6;TYPE=snp\tGT:D'..b'E=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:5:3,2:3:135:2:53:0,-3.93517\n+phiX174\t2828\t.\tT\tG\t4.53266e-10\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=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31;NS=1;NUMALT=1;ODDS=22.9831;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=348;RO=6;RPL=0;RPP=7.35324;RPPR=4.45795;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:8:6,2:6:348:2:100:0,-10.3385\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;PRO=0;QA=57;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:5:3,2:3:150:2:57:0,-4.26987\n+phiX174\t3155\t.\tT\tG\t1.16474e-06\t.\tAB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=15.1316;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPL=1;RPP=3.0103;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp\tGT:DP:AD:RO:QR:AO:QA:GL\t0:7:5,2:5:299:2:75:0,-7.18392\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\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\t3729\t.\tC\tT\t6.17726e-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=18.0684;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;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\t0:6:4,2:4:232:2:61:0,-8.44905\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' 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