| Previous changeset 6:7253b367c082 (2021-10-11) Next changeset 8:1a56888ddb7d (2021-10-11) |
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Commit message:
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303" |
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modified:
arriba.xml macros.xml test-data/fusions.tsv |
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added:
arriba_draw_fusions.xml |
| b |
| diff -r 7253b367c082 -r 25d207f7ff83 arriba.xml --- a/arriba.xml Mon Oct 11 01:47:22 2021 +0000 +++ b/arriba.xml Mon Oct 11 16:40:51 2021 +0000 |
| b |
| b'@@ -55,7 +55,7 @@\n #end if\n #end if\n -a \'$genome_assembly\'\n- -g \'$gtf\'\n+ -g \'$annotation\'\n #if $blacklist\n -b \'$blacklist\'\n #else\n@@ -155,57 +155,8 @@\n && samtools index Aligned.sortedByCoord.out.bam\n #end if\n #if str($visualization.do_viz) == "yes"\n-&& draw_fusions.R \n- --fusions=fusions.tsv \n- --alignments=Aligned.sortedByCoord.out.bam \n- --annotation=\'$gtf\'\n- --output=fusions.pdf \n- #if $visualization.cytobands\n- --cytobands=\'$visualization.cytobands\'\n- #end if\n- #if $protein_domains\n- --proteinDomains=\'$protein_domains\'\n- #end if\n- ## Visualization Options\n- #if $visualization.options.transcriptSelection\n- --transcriptSelection=$visualization.options.transcriptSelection\n- #end if\n- #if $visualization.options.minConfidenceForCircosPlot\n- --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot\n- #end if\n- #if $visualization.options.showIntergenicVicinity\n- --showIntergenicVicinity=$visualization.options.showIntergenicVicinity\n- #end if\n- #if $visualization.options.squishIntrons\n- --squishIntrons=$visualization.options.squishIntrons\n- #end if\n- #if $visualization.options.mergeDomainsOverlappingBy\n- --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy\n- #end if\n- #if $visualization.options.printExonLabels\n- --printExonLabels=$visualization.options.printExonLabels\n- #end if\n- #if $visualization.options.render3dEffect\n- --render3dEffect=$visualization.options.render3dEffect\n- #end if\n- #if $visualization.options.optimizeDomainColors\n- --optimizeDomainColors=$visualization.options.optimizeDomainColors\n- #end if\n- #if $visualization.options.color1\n- --color1=$visualization.options.color1\n- #end if\n- #if $visualization.options.color2\n- --color2=$visualization.options.color2\n- #end if\n- #if $visualization.options.pdfWidth\n- --pdfWidth=$visualization.options.pdfWidth\n- #end if\n- #if $visualization.options.pdfHeight\n- --pdfHeight=$visualization.options.pdfHeight\n- #end if\n- #if $visualization.options.fontSize\n- --fontSize=$visualization.options.fontSize\n- #end if\n+#set $fusions = \'fusions.tsv\'\n+&& @DRAW_FUSIONS@\n #end if\n ]]></command>\n <inputs>\n@@ -243,7 +194,7 @@\n </when>\n </conditional>\n <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/>\n- <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/>\n+ <param name="annotation" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/>\n <param name="blacklist" argument="-b" type="data" format="tabular,tabular.gz" optional="true" label="File containing blacklisted ranges."/>\n <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>\n <param name="known_fusions" argument="-k" type="data" format="tabular,tabular.gz" optional="true" label="File containing known fusions">\n@@ -433,120 +384,15 @@\n <option value="no">no</option>\n </param>\n <when value="yes">\n- <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>\n- <section name="options" expanded="false" title="Visualization Options">\n- <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">\n- <help>By default the transcript isoform with the highest coverage is drawn. \n- Alternatively, the transcript isoform that is provided in the columns \n- transcript_id1 and transcript_id2 in the given fusions file can be drawn. \n- Sel'..b' Default: FALSE\n- </help>\n- <option value="TRUE">True</option>\n- <option value="FALSE">False</option>\n- </param>\n- <param argument="--color1" type="color" value="" optional="true" label="Color of the 5\' end of the fusion."/>\n- <param argument="--color2" type="color" value="" optional="true" label="Color of the 3\' end of the fusion."/>\n- <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches"\n- help="Default: 11.692"/>\n- <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"\n- help="Default: 8.267"/>\n- <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"\n- help="Default: 1.0"/>\n- </section>\n-\n+ <expand macro="visualization_options" />\n </when>\n <when value="no"/>\n </conditional>\n \n </inputs>\n <outputs>\n- <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/>\n- <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv">\n+ <data name="fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/>\n+ <data name="discarded_fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv">\n <filter> output_fusions_discarded == "yes"</filter>\n </data> \n <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">\n@@ -564,13 +410,13 @@\n <param name="input" ftype="sam" value="Aligned.out.sam"/>\n </conditional>\n <param name="genome_assembly" ftype="fasta" value="genome.fasta"/>\n- <param name="gtf" ftype="gtf" value="genome.gtf"/>\n+ <param name="annotation" ftype="gtf" value="genome.gtf"/>\n <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>\n <conditional name="visualization">\n <param name="do_viz" value="no"/>\n <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>\n </conditional>\n- <output name="fusions">\n+ <output name="fusions_tsv">\n <assert_contents>\n <has_text_matching expression="BCR\\tABL1"/>\n </assert_contents>\n@@ -583,15 +429,22 @@\n <param name="input" ftype="sam" value="Aligned.out.sam"/>\n </conditional>\n <param name="genome_assembly" ftype="fasta" value="genome.fasta"/>\n- <param name="gtf" ftype="gtf" value="genome.gtf"/>\n+ <param name="annotation" ftype="gtf" value="genome.gtf"/>\n+ <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>\n <conditional name="visualization">\n <param name="do_viz" value="yes"/>\n+ <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>\n </conditional>\n- <output name="fusions">\n+ <output name="fusions_tsv">\n <assert_contents>\n <has_text_matching expression="BCR\\tABL1"/>\n </assert_contents>\n </output>\n+ <output name="fusions_pdf">\n+ <assert_contents>\n+ <has_size value= "64000" delta="5000" />\n+ </assert_contents>\n+ </output>\n </test>\n \n </tests>\n' |
| b |
| diff -r 7253b367c082 -r 25d207f7ff83 arriba_draw_fusions.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/arriba_draw_fusions.xml Mon Oct 11 16:40:51 2021 +0000 |
| [ |
| b'@@ -0,0 +1,282 @@\n+<tool id="arriba_draw_fusions" name="Arriba Draw Fusions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">\n+ <description></description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="version_command" />\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $alignments.extension == \'sam\'\n+ ln -sf \'$assembly\' input.fa &&\n+ samtools faidx input.fa &&\n+ samtools view -b -@ \\${GALAXY_SLOTS:-1} -t input.fa.fai \'$alignments\' | \n+ samtools sort -O bam -@ \\${GALAXY_SLOTS:-1} -T "\\${TMPDIR:-.}" -o Aligned.sortedByCoord.out.bam &&\n+ samtools index Aligned.sortedByCoord.out.bam &&\n+ #else\n+ ln -sf \'${alignments}\' \'Aligned.sortedByCoord.out.bam\' &&\n+ ln -sf \'$alignments.metadata.bam_index\' \'Aligned.sortedByCoord.out.bam.bai\' &&\n+ #end if\n+ @DRAW_FUSIONS@\n+ ]]></command>\n+ <inputs>\n+ <param argument="--fusions" type="data" format="tabular" label="Arriba fusions.tsv"/>\n+ <param argument="--alignments" type="data" format="sam,bam" label="STAR Aligned.out.bam"/>\n+ <param name="assembly" type="data" format="fasta" optional="true" label="Genome assembly fasta (required when alignments are not sorted bam format)"/>\n+ <param argument="--annotation" type="data" format="gtf" label="GTF file with gene annotation"/>\n+ <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>\n+ <section name="visualization" expanded="true" title="Visualization Options">\n+ <expand macro="visualization_options" />\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">\n+ <filter>visualization[\'do_viz\'] == "yes"</filter>\n+ </data> \n+ </outputs>\n+ <tests>\n+ <!-- Test 1 - From exisitng BAM -->\n+ <test> \n+ <param name="fusions" ftype="tabular" value="fusions.tsv"/>\n+ <param name="alignments" ftype="sam" value="Aligned.out.sam"/>\n+ <param name="assembly" ftype="fasta" value="genome.fasta"/>\n+ <param name="annotation" ftype="gtf" value="genome.gtf"/>\n+ <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>\n+ <section name="visualization">\n+ <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>\n+ </section>\n+ <output name="fusions_pdf">\n+ <assert_contents>\n+ <has_size value="64000" delta="5000" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**Arriba**\n+\n+\n+Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.\n+It is based on chimeric alignments found by the STAR RNA-Seq aligner.\n+\n+\n+**INPUTS**\n+\n+See: https://arriba.readthedocs.io/en/latest/input-files/\n+\n+ - Alignments\n+\n+ Arriba takes the main output file of STAR (Aligned.out.bam) as input (parameter -x). If STAR was run with the parameter --chimOutType WithinBAM, then this file contains all the information needed by Arriba to find fusions. When STAR was run with the parameter --chimOutType SeparateSAMold, the main output file lacks chimeric alignments. Instead, STAR writes them to a separate output file named Chimeric.out.sam. In this case, the file needs to be passed to Arriba via the parameter -c in addition to the main output file Aligned.out.bam.\n+\n+ Arriba extracts three types of reads from the alignment file(s):\n+\n+ * Split-reads, i.e., reads composed of segments which map in a non-linear way. STAR stores such reads as supplementary alignments.\n+ * Discordant mates, i.e., paired-end reads which originate from the same fragment but which align in a non-linear way.\n+ * A'..b'I is used, then an attempt is made to fill missing information with the assembly sequence. A sequence stretch that was taken from the assembly sequence rather than the supporting reads is wrapped in parentheses (( and )). In addition, when -I is used, the sequence is trimmed to the boundaries of the fused transcripts. The coordinate of the fusion breakpoint relative to the start of the transcript can thus easily be inferred by counting the bases from the beginning of the fusion transcript to the breakpoint character (|). In case the full sequence could be constructed from the combined information of supporting reads and assembly sequence, the start of the fusion transcript is marked by a caret sign (^) and the end by a dollar sign ($). If the full sequence could not be constructed, these signs are missing.\n+\n+ * peptide_sequence : This column contains the fusion peptide sequence. The sequence is translated from the fusion transcript given in the column fusion_transcript and determines the reading frame of the fused genes according to the transcript isoforms given in the columns transcript_id1 and transcript_id2. Translation starts at the start of the assembled fusion transcript or when the start codon is encountered in the 5\' gene. Translation ends when either the end of the assembled fusion transcript is reached or when a stop codon is encountered. If the fusion transcript contains an ellipsis (...), the sequence beyond the ellipsis is trimmed before translation, because the reading frame cannot be determined reliably. The column contains a dot (.), when the transcript sequence could not be predicted or when the precise breakpoints are unknown due to lack of split reads or when the fusion transcript does not overlap any coding exons in the 5\' gene or when no start codon could be found in the 5\' gene or when there is a stop codon prior to the fusion junction (in which case the column reading_frame contains the value stop-codon). The breakpoint is represented as a pipe symbol (|). If a codon spans the breakpoint, the amino acid is placed on the side of the breakpoint where two of the three bases reside. Codons resulting from non-template bases are flanked by two pipes. Amino acids are written as lowercase characters in the following situations: non-silent SNVs/SNPs, insertions, frameshifts, codons spanning the breakpoint, non-coding regions (introns/intergenic regions/UTRs), and non-template bases. Codons which cannot be translated to amino acids, such as those having invalid characters, are represented as ?.\n+\n+ * read_identifiers : This column contains the names of the supporting reads separated by commas.\n+\n+ - fusions.discarded.tsv\n+\n+ The file fusions.discarded.tsv (as specified by the parameter -O) contains all events that Arriba classified as an artifact or that are also observed in healthy tissue. It has the same format as the file fusions.tsv. \n+\n+\n+**VISUALIZATION**\n+\n+See: https://arriba.readthedocs.io/en/latest/visualization/\n+\n+ - fusions.pdf\n+\n+ A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint.\n+\n+\n+**OPTIONS**\n+\n+ - Arriba: https://arriba.readthedocs.io/en/latest/command-line-options/#arriba\n+ - Visualization: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr\n+ - RNA STAR: https://arriba.readthedocs.io/en/latest/workflow/\n+\n+\n+.. _Arriba: https://arriba.readthedocs.io/en/latest/\n+.. _INPUTS: https://arriba.readthedocs.io/en/latest/input-files/\n+.. _OUTPUTS: https://arriba.readthedocs.io/en/latest/output-files/\n+.. _VISUALIZATION: https://arriba.readthedocs.io/en/latest/visualization/\n+.. _OPTIONS: https://arriba.readthedocs.io/en/latest/command-line-options/\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 7253b367c082 -r 25d207f7ff83 macros.xml --- a/macros.xml Mon Oct 11 01:47:22 2021 +0000 +++ b/macros.xml Mon Oct 11 16:40:51 2021 +0000 |
| b |
| b'@@ -1,7 +1,6 @@\n <macros>\n <token name="@TOOL_VERSION@">2.1.0</token>\n <token name="@VERSION_SUFFIX@">0</token>\n-dd\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>\n@@ -17,4 +16,164 @@\n <xml name="version_command">\n <version_command>arriba -h | grep Version | sed \'s/^.* //\'</version_command>\n </xml>\n+ <xml name="visualization_options">\n+ <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>\n+ <section name="options" expanded="false" title="Draw Fusion Options">\n+ <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">\n+ <help>By default the transcript isoform with the highest coverage is drawn.\n+ Alternatively, the transcript isoform that is provided in the columns\n+ transcript_id1 and transcript_id2 in the given fusions file can be drawn.\n+ Selecting the isoform with the highest coverage usually produces nicer plots,\n+ in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint.\n+ However, the isoform with the highest coverage may not be the one that is involved in the fusion.\n+ Often, genomic rearrangements lead to non-canonical isoforms being transcribed.\n+ For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2,\n+ which reflect the actual isoforms involved in a fusion.\n+\\ As a third option, the transcripts that are annotated as canonical can be drawn.\n+ Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical.\n+ </help>\n+ <option value="coverage">coverage</option>\n+ <option value="provided">provided</option>\n+ <option value="canonical">canonical</option>\n+ </param>\n+ <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection">\n+ <help>The fusion of interest is drawn as a solid line in the circos plot.\n+ To give an impression of the overall degree of rearrangement,\n+ all other fusions are drawn as semi-transparent lines in the background.\n+ This option determines which other fusions should be included in the circos plot.\n+ Values specify the minimum confidence a fusion must have to be included.\n+ It usually makes no sense to include low-confidence fusions in circos plots,\n+ because they are abundant and unreliable, and would clutter up the circos plot.\n+ Default: medium\n+ </help>\n+ <option value="none">none - only the fusion of interest is drawn</option>\n+ <option value="low">low</option>\n+ <option value="medium">medium</option>\n+ <option value="high">high</option>\n+ </param>\n+ <param argument="--showIntergenicVicinity" type="integer" value="" min="0" optional="true" label="Intergenic Vicinity">\n+ <help>This option only applies to intergenic breakpoints.\n+ If it is set to a value greater than 0, then the script draws the genes\n+ which are no more than the given distance away from an inter'..b't="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors">\n+ <help>By default, the script colorizes domains according to the colors\n+ specified in the file given in --annotation.\n+ This way, coloring of domains is consistent across all proteins.\n+ But since there are more distinct domains than colors,\n+ this can lead to different domains having the same color.\n+ If this option is set to TRUE, the colors are recomputed for each fusion separately.\n+ This ensures that the colors have the maximum distance for each individual fusion,\n+ but they are no longer consistent across different fusions.\n+ Default: FALSE\n+ </help>\n+ <option value="TRUE">True</option>\n+ <option value="FALSE">False</option>\n+ </param>\n+ <param argument="--color1" type="color" value="" optional="true" label="Color of the 5\' end of the fusion."/>\n+ <param argument="--color2" type="color" value="" optional="true" label="Color of the 3\' end of the fusion."/>\n+ <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches"\n+ help="Default: 11.692"/>\n+ <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"\n+ help="Default: 8.267"/>\n+ <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"\n+ help="Default: 1.0"/>\n+ </section>\n+ </xml>\n+ <token name="@DRAW_FUSIONS@">\n+draw_fusions.R\n+ --fusions=\'$fusions\'\n+ --alignments=\'Aligned.sortedByCoord.out.bam\'\n+ --annotation=\'$annotation\'\n+ --output=fusions.pdf\n+ #if $visualization.cytobands\n+ --cytobands=\'$visualization.cytobands\'\n+ #end if\n+ #if $protein_domains\n+ --proteinDomains=\'$protein_domains\'\n+ #end if\n+ ## Visualization Options\n+ #if $visualization.options.transcriptSelection\n+ --transcriptSelection=$visualization.options.transcriptSelection\n+ #end if\n+ #if $visualization.options.minConfidenceForCircosPlot\n+ --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot\n+ #end if\n+ #if $visualization.options.showIntergenicVicinity\n+ --showIntergenicVicinity=$visualization.options.showIntergenicVicinity\n+ #end if\n+ #if $visualization.options.squishIntrons\n+ --squishIntrons=$visualization.options.squishIntrons\n+ #end if\n+ #if $visualization.options.mergeDomainsOverlappingBy\n+ --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy\n+ #end if\n+ #if $visualization.options.printExonLabels\n+ --printExonLabels=$visualization.options.printExonLabels\n+ #end if\n+ #if $visualization.options.render3dEffect\n+ --render3dEffect=$visualization.options.render3dEffect\n+ #end if\n+ #if $visualization.options.optimizeDomainColors\n+ --optimizeDomainColors=$visualization.options.optimizeDomainColors\n+ #end if\n+ #if $visualization.options.color1\n+ --color1=$visualization.options.color1\n+ #end if\n+ #if $visualization.options.color2\n+ --color2=$visualization.options.color2\n+ #end if\n+ #if $visualization.options.pdfWidth\n+ --pdfWidth=$visualization.options.pdfWidth\n+ #end if\n+ #if $visualization.options.pdfHeight\n+ --pdfHeight=$visualization.options.pdfHeight\n+ #end if\n+ #if $visualization.options.fontSize\n+ --fontSize=$visualization.options.fontSize\n+ #end if\n+</token>\n </macros>\n' |
| b |
| diff -r 7253b367c082 -r 25d207f7ff83 test-data/fusions.tsv --- a/test-data/fusions.tsv Mon Oct 11 01:47:22 2021 +0000 +++ b/test-data/fusions.tsv Mon Oct 11 16:40:51 2021 +0000 |
| b |
| @@ -1,2 +1,2 @@ #gene1 gene2 strand1(gene/fusion) strand2(gene/fusion) breakpoint1 breakpoint2 site1 site2 type split_reads1 split_reads2 discordant_mates coverage1 coverage2 confidence reading_frame tags retained_protein_domains closest_genomic_breakpoint1 closest_genomic_breakpoint2 gene_id1 gene_id2 transcript_id1 transcript_id2 direction1 direction2 filters fusion_transcript peptide_sequence read_identifiers -BCR ABL1 +/+ +/+ 22:23632600 9:133729451 CDS/splice-site CDS/splice-site translocation 4 7 0 4 12 high in-frame Mitelman Bcr-Abl_oncoprotein_oligomerisation_domain(100%),C2_domain(100%),PH_domain(100%),RhoGEF_domain(100%)|F-actin_binding(100%),Protein_kinase_domain(100%),SH2_domain(100%),SH3_domain(100%),Variant_SH3_domain(100%) . . ENSG00000186716.15 ENSG00000097007.13 ENST00000305877.8 ENST00000372348.2 downstream upstream . AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAG___ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA|AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAG___GTGAAAAGCTCCGGG SFSLTSVELQMLTNSCVKLQTVHSIPLTINKEDDESPGLYGFLNVIVHSATGFKQSS|kALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLR BCR-ABL1-10,BCR-ABL1-2,BCR-ABL1-24,BCR-ABL1-28,BCR-ABL1-58,BCR-ABL1-60,BCR-ABL1-76,BCR-ABL1-12,BCR-ABL1-18,BCR-ABL1-4,BCR-ABL1-66 +BCR ABL1 +/+ +/+ 22:230999 9:275100 CDS/splice-site CDS/splice-site translocation 1 3 0 3 8 low in-frame . Bcr-Abl_oncoprotein_oligomerisation_domain(100%),C2_domain(100%),RhoGEF_domain(100%)|F-actin_binding(100%),Protein_kinase_domain(100%),SH2_domain(100%),SH3_domain(100%) . . ENSG00000186716 ENSG00000097007 ENST00000305877 ENST00000372348 downstream upstream . AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAG___ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA|AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAG___GTGAAAAGCTCCGGG SFSLTSVELQMLTNSCVKLQTVHSIPLTINKEDDESPGLYGFLNVIVHSATGFKQSS|kALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLR BCR-ABL1-4,BCR-ABL1-28,BCR-ABL1-60,BCR-ABL1-76 |