| Previous changeset 22:99684adf84de (2015-10-09) Next changeset 24:da6e10dee68b (2016-09-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd |
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modified:
freebayes.xml leftalign.xml test-data/freebayes-phix174-test1.vcf test-data/freebayes-phix174-test2.vcf |
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added:
test-data/freebayes-phix174-test3.vcf test-data/freebayes-phix174-test4.vcf |
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removed:
tool_dependencies.xml |
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| diff -r 99684adf84de -r 52aed7d9ed2b freebayes.xml --- a/freebayes.xml Fri Oct 09 17:20:08 2015 -0400 +++ b/freebayes.xml Sun Sep 25 09:48:24 2016 -0400 |
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| b'@@ -1,537 +1,674 @@\n-<?xml version="1.0"?>\n-<tool id="freebayes" name="FreeBayes" version="0.4.1">\n- <requirements>\n- <requirement type="package" version="0_9_20_b040236">freebayes</requirement>\n- <requirement type="package" version="0.1.18">samtools</requirement>\n- </requirements>\n- <description> - bayesian genetic variant detector</description>\n- <command>\n+<tool id="freebayes" name="FreeBayes" version="1.0.2.29--1">\n+ <description> - bayesian genetic variant detector</description>\n+ <requirements>\n+ <requirement type="package" version="1.0.2.29">freebayes</requirement>\n+ <requirement type="package" version="0.1.19">samtools</requirement>\n+ <requirement type="package" version="4.1.3">gawk</requirement>\n+ <requirement type="package" version="20160622">parallel</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command>\n+<![CDATA[\n ##set up input files\n \n #set $reference_fasta_filename = "localref.fa"\n- \n+\n #if str( $reference_source.reference_source_selector ) == "history":\n- ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&\n- samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&\n+ ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&\n+ samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&\n #else:\n #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )\n #end if\n- \n+\n #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):\n- ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&\n- ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&\n+ ln -s "${input_bam}" "b_${bam_count}.bam" &&\n+ ln -s "${input_bam.metadata.bam_index}" "b_${bam_count}.bam.bai" &&\n #end for\n- \n+\n ## Tabixize optional input_varinat_vcf file (for --variant-input option)\n- \n- #if ( str( $options_type.options_type_selector ) == \'cline\' or str( $options_type.options_type_selector ) == \'full\' ) and $options_type.optional_inputs.optional_inputs_selector and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":\n- ln -s "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &&\n- ln -s "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &&\n+ #if ( str( $options_type.options_type_selector ) == \'cline\' or str( $options_type.options_type_selector ) == \'full\' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == \'set\' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":\n+ ln -s "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &&\n+ ln -s "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &&\n #end if\n- \n- ##finished setting up inputs\n- \n- ##COMMAND LINE STARTS HERE\n- \n- freebayes\n+\n #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):\n- --bam "localbam_${bam_count}.bam"\n+ samtools view -H b_${bam_count}.bam | grep "^@SQ" | cut -f 2- | awk \'{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\\t0\\t"$2; }\' >> regions_all.bed &&\n #end for\n- --fasta-reference "${reference_fasta_filename}"\n- \n- ##outputs\n- --vcf "${output_vcf}"\n- \n+\n+ sort -u regions_all.bed > regions_uniq.bed &&\n+ ## split into even small chunks, this has some disatvantages and will not be used for the moment\n+ ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&\n+\n+ mkdir vcf_output &&\n+ mkdir failed_alleles &&\n+ mkdir trace &&\n+\n+ ## Finished setting up inpu'..b'me} on ${on_string} (failed alleles)">\n+ <filter>( options_type[\'options_type_selector\'] == \'cline\' or options_type[\'options_type_selector\'] == \'full\' ) and options_type[\'optional_inputs\'][\'optional_inputs_selector\'] == \'set\' and options_type[\'optional_inputs\'][\'output_failed_alleles_option\'] is True</filter>\n+ </data>\n+ <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">\n+ <filter>( options_type[\'options_type_selector\'] == \'cline\' or options_type[\'options_type_selector\'] == \'full\' ) and options_type[\'optional_inputs\'][\'optional_inputs_selector\'] == \'set\' and options_type[\'optional_inputs\'][\'output_trace_option\'] is True</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>\n+ <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>\n+ <param name="options_type_selector" value="simple"/>\n+ <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>\n+ </test>\n+ <test>\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>\n+ <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>\n+ <param name="options_type_selector" value="naive_w_filters"/>\n+ <param name="min_coverage" value="14"/>\n+ <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>\n+ </test>\n+ <test>\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>\n+ <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>\n+ <param name="options_type_selector" value="naive_w_filters"/>\n+ <param name="min_coverage" value="14"/>\n+ <output name="output_vcf" file="freebayes-phix174-test3.vcf" compare="contains"/>\n+ </test>\n+ <test>\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>\n+ <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>\n+ <param name="options_type_selector" value="full"/>\n+ <param name="population_model_selector" value="set"/>\n+ <param name="P" value="1"/>\n+ <output name="output_vcf" file="freebayes-phix174-test4.vcf" compare="contains"/>\n+ </test>\n+ </tests>\n+ <help>\n **What it does**\n \n FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.\n \n See https://github.com/ekg/freebayes for details on FreeBayes.\n \n-This Galaxy instance of FreeBayes corresponds to release 0.9.20\n-\n ------\n \n **Description**\n@@ -813,16 +950,16 @@\n For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing <http://arxiv.org/abs/1207.3907>`_.\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- \n- <citations>\n- <citation type="bibtex">@misc{1207.3907,\n+ </help>\n+ <citations>\n+ <citation type="bibtex">@misc{1207.3907,\n Author = {Erik Garrison},\n Title = {Haplotype-based variant detection from short-read sequencing},\n Year = {2012},\n Eprint = {arXiv:1207.3907},\n url = {http://arxiv.org/abs/1207.3907},\n }</citation>\n- </citations>\n+ </citations>\n </tool>\n' |
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| diff -r 99684adf84de -r 52aed7d9ed2b leftalign.xml --- a/leftalign.xml Fri Oct 09 17:20:08 2015 -0400 +++ b/leftalign.xml Sun Sep 25 09:48:24 2016 -0400 |
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| @@ -1,85 +1,83 @@ <?xml version="1.0"?> -<tool id="bamleftalign" name="BamLeftAlign" version="0.4"> - <requirements> - <requirement type="package" version="0_9_20_b040236">freebayes</requirement> - <requirement type="package" version="0.1.18">samtools</requirement> - </requirements> - <description> indels in BAM datasets</description> - <command> - ##set up input files - #set $reference_fasta_filename = "localref.fa" - #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && - samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for leftalign" >&2 && - #else: - #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) - #end if +<tool id="bamleftalign" name="BamLeftAlign" version="1.0.2.29"> + <description> indels in BAM datasets</description> + <requirements> + <requirement type="package" version="1.0.2.29">freebayes</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + ##set up input files + #set $reference_fasta_filename = "localref.fa" + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for leftalign" >&2 && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if - ##finished setting up inputs - - ##start leftalign commandline - samtools view -bh "${input_bam}" | bamleftalign - --fasta-reference "${reference_fasta_filename}" - -c - --max-iterations "${iterations}" - ##outputs - > "${output_bam}" - </command> - <inputs> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> - <option value="cached">Locally cached</option> - <option value="history">History</option> - </param> - <when value="cached"> - <param name="input_bam" type="data" format="bam" label="Select BAM dataset to leftalign"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + ##finished setting up inputs + + ##start leftalign commandline + samtools view -bh "${input_bam}" | bamleftalign + --fasta-reference "${reference_fasta_filename}" + -c + --max-iterations "${iterations}" + ##outputs + > "${output_bam}" + </command> + <inputs> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> + <option value="cached">Locally cached</option> + <option value="history">History</option> </param> - <param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="fasta_indexes"></options> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> - </param> - </when> - <when value="history"> - <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> - </when> - </conditional> - <param name="iterations" type="integer" value="5" label="Maximum number of iterations" help="Iterate the left-realignment no more than this many times" /> - </inputs> - <outputs> - <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (alignments)" /> - </outputs> - <tests> - <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="leftalign.fa"/> - <param name="input_bam" ftype="bam" value="left-align-input.bam"/> - <param name="iterations" value="5"/> - <output name="output_bam" file="left-align-output.bam" /> - </test> - </tests> - <stdio> - <exit_code range="1:" /> - </stdio> - <help> + <when value="cached"> + <param name="input_bam" type="data" format="bam" label="Select BAM dataset to leftalign"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> + </param> + <param name="ref_file" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + <param name="iterations" type="integer" value="5" label="Maximum number of iterations" help="Iterate the left-realignment no more than this many times" /> + </inputs> + <outputs> + <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (alignments)" /> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="leftalign.fa"/> + <param name="input_bam" ftype="bam" value="left-align-input.bam"/> + <param name="iterations" value="5"/> + <output name="output_bam" file="left-align-output.bam" /> + </test> + </tests> + <help> When calling indels, it is important to homogenize the positional distribution of insertions and deletions in the input by using left realignment. Left realignment will place all indels in homopolymer and microsatellite repeats at the same position, provided that doing so does not introduce mismatches between the read and reference other than the indel. This method is computationally inexpensive and handles the most common classes of alignment inconsistency. This is leftalign utility from FreeBayes package developed and maintained by Erik Garrison (https://github.com/ekg/freebayes). - </help> - - <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} - } - </citation> - </citations> - + </help> + <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} + } + </citation> + </citations> </tool> |
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| diff -r 99684adf84de -r 52aed7d9ed2b test-data/freebayes-phix174-test1.vcf --- a/test-data/freebayes-phix174-test1.vcf Fri Oct 09 17:20:08 2015 -0400 +++ b/test-data/freebayes-phix174-test1.vcf Sun Sep 25 09:48:24 2016 -0400 |
| b |
| b'@@ -1,26 +1,85 @@\n-phiX174\t311\t.\tA\tG\t6.48411\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=1.23853;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:RO:QR:AO:QA:GL\t0/1:9:7:478:2:70:-5.49703,0,-42.5499\n-phiX174\t374\t.\tT\tG\t30.6931\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=7.0665;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:RO:QR:AO:QA:GL\t0/1:4:2:141:2:75:-6.69903,0,-12.969\n-phiX174\t913\t.\tA\tC\t13.1703\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=2.98318;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:RO:QR:AO:QA:GL\t0/1:5:3:171:2:58:-5.00485,0,-15.4549\n-phiX174\t1205\t.\tA\tC\t2.30262\t.\tAB=0;ABP=0;AC=0;AF=0;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=0.357718;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:DP:RO:QR:AO:QA:GL\t0/0:10:8:456:2:67:-5.00791,0,-40.2529\n-phiX174\t1245\t.\tG\tT\t6.48411\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=31;MQMR=28.4286;NS=1;NUMALT=1;ODDS=1.23853;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=389;RO=7;RPL=2;RPP=7.35324;RPPR=3.32051;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=18.2106;SRR=7;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:7:389:2:70:-5.49703,0,-34.4127\n-phiX174\t1249\t.\tT\tG\t15.3287\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=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=30.1429;NS=1;NUMALT=1;ODDS=3.4998;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=464;RO=7;RPL=1;RPP=3.0103;RPPR=5.80219;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=5.80219;SRR=5;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:9:7:464:2:74:-5.87703,0,-41.2699\n-phiX174\t1445\t.\tC\tA\t24.4745\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=5.63189;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:RO:QR:AO:QA:GL\t0/1:7:5:273:2:76:-6.43501,0,-24.331\n-phiX174\t1577\t.\tA\tC\t4.06305\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=0.437365;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:RO:QR:AO:QA:GL\t0/1:9:7:460:2:60:-4.54703,0,-40.9042\n-phiX174\t1631\t.\tT\tG\t2.719\t.\tAB=0;ABP=0;AC=0;AF=0;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=0.138972;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:RO:QR:AO:QA:GL\t0/0:10:8:500:2:68:-5.10291,0,-44.2679\n-phiX174\t1772\t.\tT\tG\t2.16317\t.\tAB=0;ABP=0;AC=0;AF=0;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=0.437618;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;S'..b'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:DPR:RO:QR:AO:QA:GL\t0/1:5:5,2:3:150:2:57:-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:DPR:RO:QR:AO:QA:GL\t0/1:9:9,3:6:361:3:94:-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:DPR:RO:QR:AO:QA:GL\t0/1:7:7,2:5:299:2:75:-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:DPR:RO:QR:AO:QA:GL\t0/1:6:6,2:4:284:2:58:-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:DPR:RO:QR:AO:QA:GL\t0/1:10:10,2:8:526:2:60:-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:DPR:RO:QR:AO:QA:GL\t0/1:6:6,2:4:232:2:61:-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:DPR:RO:QR:AO:QA:GL\t0/1:8:8,2:6:322:2:85:-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:DPR:RO:QR:AO:QA:GL\t0/1:6:6,2:4:284:2:55:-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:DPR:RO:QR:AO:QA:GL\t0/1:6:6,2:4:204:2:59:-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:DPR:RO:QR:AO:QA:GL\t0/1:6:6,2:4:193:2:70:-2.81796,0,-11.1489\n' |
| b |
| diff -r 99684adf84de -r 52aed7d9ed2b test-data/freebayes-phix174-test2.vcf --- a/test-data/freebayes-phix174-test2.vcf Fri Oct 09 17:20:08 2015 -0400 +++ b/test-data/freebayes-phix174-test2.vcf Sun Sep 25 09:48:24 2016 -0400 |
| b |
| b'@@ -1,19 +1,78 @@\n-phiX174\t1134\t.\tA\t.\t1.75185e-15\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:RO:QR:AO:QA:GL\t0/0:14:14:916:.:.:0\n-phiX174\t1135\t.\tC\t.\t1.75538e-15\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:RO:QR:AO:QA:GL\t0/0:14:14:957:.:.:0\n-phiX174\t1136\t.\tG\t.\t1.75185e-15\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:RO:QR:AO:QA:GL\t0/0:14:14:919:.:.:0\n-phiX174\t1137\t.\tC\t.\t1.75349e-15\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:RO:QR:AO:QA:GL\t0/0:14:14:927:.:.:0\n-phiX174\t1138\t.\tC\t.\t1.75538e-15\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:RO:QR:AO:QA:GL\t0/0:14:14:876:.:.:0\n-phiX174\t1139\t.\tG\t.\t1.75538e-15\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:RO:QR:AO:QA:GL\t0/0:14:14:946:.:.:0\n-phiX174\t1140\t.\tT\t.\t6.10945e-16\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:RO:QR:AO:QA:GL\t0/0:15:15:927:.:.:0\n-phiX174\t1141\t.\tT\tG\t0.000113755\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=10.55;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:RO:QR:AO:QA:GL\t0/0:15:14:880:1:50:-1.66064,0,-76.4892\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:RO:QR:AO:QA:GL\t0/0:16:16:1082:.:.: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:RO:QR:AO:QA:GL\t0/0:16:16:1029:.:.: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:RO:QR:AO:QA:GL\t0/0:16:16:1114:.:.:0\n-phiX174\t1145\t.\tG\t.\t6.0859e-16\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:RO:QR:AO:QA:GL\t0/0:15:15:1042:.:.:0\n-phiX174\t1146\t.\tC\t.\t6.0859e-16\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:RO:QR:AO:QA:GL\t0/0:15:15:1058:.:.:0\n-phiX174\t1147\t.\tT\t.\t6.10945e-16\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:RO:QR:AO:QA:GL\t0/0:15:15:999:.:.:0\n-phiX174\t1148\t.\tC\t.\t6.10945e-16\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:RO:QR:AO:QA:GL\t0/0:15:15:1003:.:.:0\n-phiX174\t1149\t.\tT\tC\t7.90879e-06\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=13.2161;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:RO:QR:AO:QA:GL\t0/0:14:13:830:1:33:-0.231708,0,-72.2702\n-phiX174\t1151\t.\tC\tT\t5.70134e-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=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=15.8459;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:RO:QR:AO:QA:GL\t0/0:15:14:946:1:27:0,-0.639359,-83.1157\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:RO:QR:AO:QA:GL\t0/0:16:16:993:.:.:0\n-phiX174\t1153\t.\tT\t.\t0\t.\tDP=15;DPB=15;EP'..b'0/0:14:14:14:916:.:.: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;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:DPR:RO:QR:AO:QA:GL\t0/0:15:15,1:14:880:1:50:0,-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:DPR: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:DPR: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:DPR: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:DPR: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:DPR: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:DPR: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:DPR: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:DPR:RO:QR:AO:QA:GL\t0/0:14:14,1:13:830:1:33:0,-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:DPR:RO:QR:AO:QA:GL\t0/0:15:15,1:14:946:1:27:0,-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:DPR: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:DPR:RO:QR:AO:QA:GL\t0/0:15:15:15:880:.:.:0\n' |
| b |
| diff -r 99684adf84de -r 52aed7d9ed2b test-data/freebayes-phix174-test3.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-phix174-test3.vcf Sun Sep 25 09:48:24 2016 -0400 |
| b |
| b'@@ -0,0 +1,78 @@\n+##fileformat=VCFv4.1\n+##reference=localref.fa\n+##contig=<ID=phiX174,length=5386>\n+##phasing=none\n+##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"\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="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=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 betwe'..b'0/0:14:14:14:916:.:.: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;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:DPR:RO:QR:AO:QA:GL\t0/0:15:15,1:14:880:1:50:0,-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:DPR: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:DPR: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:DPR: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:DPR: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:DPR: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:DPR: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:DPR: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:DPR:RO:QR:AO:QA:GL\t0/0:14:14,1:13:830:1:33:0,-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:DPR:RO:QR:AO:QA:GL\t0/0:15:15,1:14:946:1:27:0,-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:DPR: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:DPR:RO:QR:AO:QA:GL\t0/0:15:15:15:880:.:.:0\n' |
| b |
| diff -r 99684adf84de -r 52aed7d9ed2b test-data/freebayes-phix174-test4.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-phix174-test4.vcf Sun Sep 25 09:48:24 2016 -0400 |
| b |
| b'@@ -0,0 +1,84 @@\n+##fileformat=VCFv4.1\n+##reference=localref.fa\n+##contig=<ID=phiX174,length=5386>\n+##phasing=none\n+##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf --theta 0.001 --ploidy 1"\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="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=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,Number=A,Type=Float,Description'..b'DPR:RO:QR:AO:QA:GL\t0:5:5,2:3:135:2:53:0,-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:DPR:RO:QR:AO:QA:GL\t0:8:8,2:6:348:2:100:0,-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:DPR:RO:QR:AO:QA:GL\t0:5:5,2:3:150:2:57:0,-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:DPR:RO:QR:AO:QA:GL\t0:7:7,2:5:299:2:75:0,-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:DPR:RO:QR:AO:QA:GL\t0:6:6,2:4:284:2:58:0,-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:DPR:RO:QR:AO:QA:GL\t0:10:10,2:8:526:2:60:0,-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:DPR:RO:QR:AO:QA:GL\t0:6:6,2:4:232:2:61:0,-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:DPR:RO:QR:AO:QA:GL\t0:8:8,2:6:322:2:85:0,-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:DPR:RO:QR:AO:QA:GL\t0:6:6,2:4:284:2:55:0,-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:DPR:RO:QR:AO:QA:GL\t0:6:6,2:4:204:2:59:0,-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:DPR:RO:QR:AO:QA:GL\t0:6:6,2:4:193:2:70:0,-8.33095\n' |
| b |
| diff -r 99684adf84de -r 52aed7d9ed2b tool_dependencies.xml --- a/tool_dependencies.xml Fri Oct 09 17:20:08 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="freebayes" version="0_9_20_b040236"> - <repository changeset_revision="059e6e3d99cc" name="package_freebayes_0_9_20_b040236" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="0.1.18"> - <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |