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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93 |
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modified:
slamdunk.xml |
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added:
alleyoop.xml macros.xml test-data/reads1.bam test-data/reads1_TCReads.bam test-data/reads1_backgroundReads.bam test-data/reads1_overallrates.csv test-data/reads1_snp.vcf test-data/reads1_tcount.tsv test-data/reads2.bam test-data/reads2_snp.vcf test-data/reads2_tcount.tsv test-data/summary.txt |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 alleyoop.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alleyoop.xml Sun Jan 20 06:51:15 2019 -0500 |
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| b'@@ -0,0 +1,168 @@\n+<tool id="alleyoop" name="Alleyoop" version="@TOOL_VERSION@">\n+ <description>- post-processing and QC of Slamdunk analyses</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <version_command>alleyoop --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+#import re\n+\n+#if $reference_source.reference_source_selector == \'history\':\n+ ln -f -s \'$reference_source.ref_file\' reference.fa &&\n+#else:\n+ ln -f -s \'$reference_source.ref_file.fields.path\' reference.fa &&\n+#end if\n+\n+mkdir ./filter &&\n+#for $bam in $reads:\n+ #set $ext = ""\n+ #set $bam_name = re.sub(\'[^\\w\\-\\.]\', \'_\', str($bam.element_identifier))\n+ #if not $bam_name.endswith(\'.bam\')\n+ #set $ext = ".bam"\n+ #end if\n+ ln -s \'$bam\' \'./filter/${bam_name}${ext}\' &&\n+ ln -s \'$bam.metadata.bam_index\' \'./filter/${bam_name}${ext}.bai\' &&\n+#end for\n+\n+mkdir ./count &&\n+#for $tsv in $count_tsvs:\n+ #set $ext = ""\n+ #set $tsv_name = re.sub(\'[^\\w\\-\\.]\', \'_\', str($tsv.element_identifier))\n+ #if not $tsv_name.endswith(\'_tcount.tsv\')\n+ #set $ext = "_tcount.tsv"\n+ #end if\n+ ln -s \'$tsv\' \'./count/${tsv_name}${ext}\' &&\n+#end for\n+\n+mkdir ./snp &&\n+#for $vcf in $variants:\n+ #set $ext = ""\n+ #set $vcf_name = re.sub(\'[^\\w\\-\\.]\', \'_\', str($vcf.element_identifier))\n+ #if not $vcf_name.endswith(\'_snp.vcf\')\n+ #set $ext = "_snp.vcf"\n+ #end if\n+ ln -s \'$vcf\' \'./snp/${vcf_name}${ext}\' &&\n+#end for\n+\n+alleyoop summary -o ./summary.txt -t ./count ./filter/*bam &&\n+\n+alleyoop rates -o ./stats -r reference.fa -mq $mq ./filter/*bam &&\n+\n+alleyoop utrrates -o ./stats -r reference.fa -b $Reference -t \\${GALAXY_SLOTS:-1} -l $l -mq $mq ./filter/*bam &&\n+\n+alleyoop tcperreadpos -o ./stats -r reference.fa -s ./snp -t \\${GALAXY_SLOTS:-1} -l $l -mq $mq ./filter/*bam &&\n+\n+alleyoop tcperutrpos -o ./stats -r reference.fa -s ./snp -t \\${GALAXY_SLOTS:-1} -l $l -b $Reference -mq $mq ./filter/*bam\n+\n+#if $bams:\n+ && alleyoop read-separator -o ./splitbams -s ./snp -r reference.fa ./filter/*bam\n+#end if\n+\n+ ]]></command>\n+ <inputs>\n+ <expand macro="reference_files" />\n+ <param name="reads" type="data" format="sam,bam" multiple="True" label="Slamdunk BAM files" />\n+ <param name="count_tsvs" type="data" format="tabular" multiple="True" label="Slamdunk Count TSV files" />\n+ <param name="variants" type="data" format="vcf" multiple="True" label="Slamdunk VCF files" />\n+ <param argument="-mq" type="integer" label="Minimum base quality"\n+ value="27" min="0"\n+ help="Minimum base quality for T>C conversions (default: 27)." />\n+ <param argument="-l" type="integer" label="Read length"\n+ value="50" min="50" help="Maximum read length (before trimming)." />\n+ <param name="bams" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output T>C separated BAM files?" help="If this option is set to Yes, the Alleyoop read-separator module will be run to output BAM files of separated T>C reads from non T>C reads. Default: No"/>\n+ </inputs>\n+ <outputs>\n+ <collection name="outputSummary" type="list" label="${tool.name} on ${on_string}: Summary tables">\n+ <discover_datasets pattern="(?P<name>.+)\\.txt$" format="tabular" directory="." visible="false" />\n+ </collection>\n+ <collection name="outputStats" type="list" label="${tool.name} on ${on_string}: Stats tables">\n+ <discover_datasets pattern="(?P<name>.+)\\.csv$" format="tabular" directory="./stats" visible="false" />\n+ </collection>\n+ <collection name="outputTCReads" type="list" label="${tool.name} on ${on_string}: TC Reads">\n+ <discover_datasets pattern="(?P<name>.+)_TCReads.bam$" format="bam" directory="./splitbams" visible="false" />\n+ <filter>bams</filter>\n+ </collection>\n+ '..b'tSummary" count="2">\n+ <element name="summary" ftype="tabular" file="summary.txt" />\n+ </output_collection>\n+ <output_collection name="outputStats" count="8">\n+ <element name="reads1_overallrates" ftype="tabular" file="reads1_overallrates.csv" />\n+ </output_collection>\n+ </test>\n+ <!-- Ensure BAM output works -->\n+ <test expect_num_outputs="4">\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="ref.fa" />\n+ <param name="Reference" ftype="bed" value="actb.bed" />\n+ <param name="reads" ftype="bam" value="reads1.bam,reads2.bam" />\n+ <param name="count_tsvs" ftype="tabular" value="reads1_tcount.tsv,reads2_tcount.tsv" />\n+ <param name="variants" ftype="vcf" value="reads1_snp.vcf,reads2_snp.vcf" />\n+ <param name="l" value="100" />\n+ <param name="mq" value="27" />\n+ <param name="bams" value="True" />\n+ <output_collection name="outputTCReads" count="2">\n+ <element name="reads1" ftype="bam" file="reads1_TCReads.bam" />\n+ </output_collection>\n+ <output_collection name="outputbkgdReads" count="2">\n+ <element name="reads1" ftype="bam" file="reads1_backgroundReads.bam" />\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+SLAMseq\n+=======\n+\n+SLAMseq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability.\n+\n+Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 <https://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4435.html>`_\n+\n+Alleyoop\n+========\n+\n+Alleyoop (Additional sLamdunk heLpEr tools for anY diagnOstics Or Plots) is a collection of tools for post-processing and running diagnostics on Slamdunk analyses. This tool works on the output of the **Slamdunk** tool and requires all the inputs listed in the table below.\n+\n+=============== ==========================================================================================================================================================\n+Parameter Description\n+=============== ==========================================================================================================================================================\n+**Genome** The reference fasta file (Genome assembly).\n+**Reference** BED-file containing coordinates for 3\' UTRs.\n+**Reads** Slamdunk Filtered BAM files.\n+**Counts** Slamdunk Count TSV files.\n+**Variants** Slandunk VCF files.\n+**Read length** Maximum length of reads (usually 50, 100, 150).\n+=============== ==========================================================================================================================================================\n+\n+This tool runs the **Alleyoop** *summary*, *rates*, *utrrates*, *tcperreadpos* and *tcperutrpos* modules and outputs:\n+\n+* Tab-separated *summary* files from the summary module with mapping and PCA statistics\n+* Tab-separated *stats* files from the rates, utrrates, tcperreadpos and tcperutrpos modules\n+\n+Optionally, the *read-separator* module can be run to output BAM files of separated T>C and non T>C reads.\n+\n+The summary and stats files can be summarised and visualised with MultiQC. An example MultiQC report can be seen here_. For information on these modules see the `Alleyoop documentation`_.\n+\n+.. _`Alleyoop documentation`: http://t-neumann.github.io/slamdunk/docs.html#document-Alleyoop\n+.. _here: http://t-neumann.github.io/slamdunk/multiqc_example/multiqc_report.html\n+\n+ ]]></help>\n+ <citations>\n+ <expand macro="citations" />\n+ </citations>\n+</tool>\n' |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Jan 20 06:51:15 2019 -0500 |
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| @@ -0,0 +1,42 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">0.3.3</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">slamdunk</requirement> + </requirements> + </xml> + <xml name="reference_files"> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Reference genome FASTA file" help="Select a built-in FASTA file (if available) or one from the history"> + <option value="cached">Use a built-in FASTA</option> + <option value="history">Use a FASTA from history</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Use built-in FASTA" help="Select genome from the list"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No reference genomes are available" /> + </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="ref_file" type="data" format="fasta" label="Use the following dataset as the FASTA" help="You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + <param name="Reference" type="data" format="bed" label="Reference 3'UTRs BED file" /> + </xml> + <xml name="citations"> + <citation type="bibtex"> + @misc{Neumann2018, + author = {Neumann, Tobias}, + year = {2018}, + title = Slamdunk}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/t-neumann/slamdunk}, +} + </citation> + </xml> +</macros> \ No newline at end of file |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 slamdunk.xml --- a/slamdunk.xml Thu Oct 11 20:33:07 2018 -0400 +++ b/slamdunk.xml Sun Jan 20 06:51:15 2019 -0500 |
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| @@ -1,8 +1,9 @@ -<tool id="slamdunk" name="Slamdunk" version="0.3.3"> +<tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy1"> <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description> - <requirements> - <requirement type="package" version="0.3.3">slamdunk</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <version_command>slamdunk --version</version_command> <command detect_errors="exit_code"><![CDATA[ #if $reference_source.reference_source_selector == 'history': @@ -30,26 +31,8 @@ '$Reads' ]]></command> <inputs> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Genome" help="Select a built-in FASTA file (if available) or one from the history"> - <option value="cached">Use a built-in FASTA</option> - <option value="history">Use a FASTA from history</option> - </param> - <when value="cached"> - <param name="ref_file" type="select" label="Use built-in FASTA" help="Select genome from the list"> - <options from_data_table="all_fasta"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No reference genomes are available" /> - </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="ref_file" type="data" format="fasta" label="Use the following dataset as the FASTA" help="You can upload a FASTA sequence to the history and use it as reference" /> - </when> - </conditional> - <param name="Reference" type="data" format="bed" /> - <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" /> + <expand macro="reference_files" /> + <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ files"/> <section name="multimapper" title="Multimapper recovery" expanded="false"> <section name="filterbed" @@ -79,8 +62,6 @@ <param name="minMQ" type="integer" min="0" value="2" label="Minimum mapping quality" help="Minimum mapping quality to consider alignments (default: 2)." /> - <param name="minMQ" type="integer" label="Minimum mapping quality" min="0" value="2" - help="Minimum mapping quality to consider alignments (default: 2)." /> <param name="minID" type="float" min="0" value="0.95" label="Minimum alignment identity" help="Minimum alignment-identity to consider alignments (default: 0.95)." /> @@ -105,11 +86,13 @@ help="Maximum read length (before trimming)." /> </inputs> <outputs> - <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" /> - <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" /> + <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" label="${tool.name} on ${on_string}: BAM"/> + <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" label="${tool.name} on ${on_string}: Count TSV"/> + <data name="outputVcf" format="vcf" from_work_dir="./out/snp/*vcf" label="${tool.name} on ${on_string}: VCF"/> </outputs> <tests> <test> + <!--Ensure default outputs work --> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="ref.fa" /> <param name="Reference" value="actb.bed" /> @@ -121,11 +104,13 @@ <section name="advanced"> <param name="minBaseQual" value="27" /> </section> - <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv" + <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/> + <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" lines_diff="2" /> + <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/> </test> <test> - <!-- test built-in fasta --> + <!--Ensure built-in fasta works --> <param name="reference_source_selector" value="cached" /> <param name="Reference" value="actb.bed" /> <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" /> @@ -136,8 +121,10 @@ <section name="advanced"> <param name="minBaseQual" value="27" /> </section> - <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv" + <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/> + <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" lines_diff="2" /> + <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -162,10 +149,13 @@ **Read length** Maximum length of reads (usually 50, 100, 150). =============== ========================================================================================================================================================== -This will run the entire *slamdunk* analysis with the most relevant output files being: +This will run the entire *slamdunk* analysis (`slamdunk all`) with the most relevant output files being: -* Tab-separated *tcount* file containing the SLAM-seq statistics per UTR -* BAM-file with the final mapped reads for visualization and further processing +* Tab-separated *tcount* file (Count TSV) containing the SLAM-seq statistics per UTR +* BAM-file with the final filtered mapped reads +* VCF file of variants called on the final filtered alignments + +These files can be input to the **Alleyoop** tool for visualization and further processing. See the `Slamdunk documentation`_ for more information. ------------------------------------------------------ @@ -198,18 +188,10 @@ **T>C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read. ============================ ================================================================================ +.. _`Slamdunk documentation`: http://t-neumann.github.io/slamdunk/docs.html ]]></help> <citations> - <citation type="bibtex"> - @misc{Neumann2018, - author = {Neumann, Tobias}, - year = {2018}, - title = Slamdunk}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/t-neumann/slamdunk}, -} - </citation> + <expand macro="citations" /> </citations> </tool> |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1.bam |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1_TCReads.bam |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1_backgroundReads.bam |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1_overallrates.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads1_overallrates.csv Sun Jan 20 06:51:15 2019 -0500 |
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| @@ -0,0 +1,7 @@ +# slamdunk rates v0.3.3 + A a C c G g T t N n +A 93 20 0 0 0 1 0 0 0 0 +C 0 0 106 12 0 0 0 0 0 0 +G 0 0 0 0 82 33 0 0 0 0 +T 0 0 4 1 0 0 102 47 0 0 +N 0 0 0 0 0 0 0 0 0 0 |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1_snp.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads1_snp.vcf Sun Jan 20 06:51:15 2019 -0500 |
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| @@ -0,0 +1,25 @@ +##fileformat=VCFv4.1 +##source=VarScan2 +##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15"> +##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)"> +##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant"> +##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant"> +##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> +##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test"> +##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)"> +##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)"> +##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> +##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> +##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> +##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 +chr5 120498 . T C . . . . . |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads1_tcount.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads1_tcount.tsv Sun Jan 20 06:51:15 2019 -0500 |
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| @@ -0,0 +1,3 @@ +Chromosome Start End Name Length Strand ConversionRate ReadsCPM Tcontent CoverageOnTs ConversionsOnTs ReadCount TcReadCount multimapCount ConversionRateLower ConversionRateUpper +chr5 120498 121492 Actb 1994 + 0.0222222222222 666666.666667 445 90 2 8 4 0 -1.0 -1.0 +chr5 120498 122492 Actb 1994 + 0.0222222222222 666666.666667 445 90 2 8 4 0 -1.0 -1.0 |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads2_snp.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads2_snp.vcf Sun Jan 20 06:51:15 2019 -0500 |
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| @@ -0,0 +1,25 @@ +##fileformat=VCFv4.1 +##source=VarScan2 +##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15"> +##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)"> +##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant"> +##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant"> +##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> +##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test"> +##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)"> +##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)"> +##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> +##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> +##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> +##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 +chr5 120499 . T C . . . . . |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/reads2_tcount.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads2_tcount.tsv Sun Jan 20 06:51:15 2019 -0500 |
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| @@ -0,0 +1,3 @@ +Chromosome Start End Name Length Strand ConversionRate ReadsCPM Tcontent CoverageOnTs ConversionsOnTs ReadCount TcReadCount multimapCount ConversionRateLower ConversionRateUpper +chr5 120498 121492 Actb 1994 + 0.0227272727273 1000000.0 445 88 2 6 3 0 -1.0 -1.0 +chr5 120498 122492 Actb 1994 + 0.0227272727273 1000000.0 445 88 2 6 3 0 -1.0 -1.0 |
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| diff -r 3fd7458bc861 -r 57bf9a0d49a5 test-data/summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary.txt Sun Jan 20 06:51:15 2019 -0500 |
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| @@ -0,0 +1,4 @@ +# slamdunk summary v0.3.3 +FileName SampleName SampleType SampleTime Sequenced Mapped Deduplicated MQ-Filtered Identity-Filtered NM-Filtered Multimap-Filtered Retained Counted Annotation +./filter/reads1.bam sample_1 NA -1 12 12 0 0 0 0 0 12 16 +./filter/reads2.bam sample_2 NA -1 6 6 0 0 0 0 0 6 12 |