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Last active November 16, 2018 19:16
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jvarkit sv2svg visualisation of a translocation.
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README.md

sv2svg http://lindenb.github.io/jvarkit/SvToSVG.html

translocation described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932280/

Identification of Balanced Chromosomal Rearrangements Previously Unknown Among Participants in the 1000 Genomes Project: Implications for Interpretation of Structural Variation in Genomes and the Future of Clinical Cytogenetics

$ samtools view -b "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG02260/alignment/HG02260.mapped.ILLUMINA.bwa.PEL.low_coverage.20130415.bam" "9:137229907-137231907" > jeter1.bam
$ samtools view -b "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG02260/alignment/HG02260.mapped.ILLUMINA.bwa.PEL.low_coverage.20130415.bam" "14:79838174-79840174" > jeter2.bam
$ samtools merge jeter3.bam jeter1.bam jeter2.bam
$ samtools index jeter3.bam
$ java -jar dist/sv2svg.jar -r "9:137229907-137231907" -r "14:79838174-79840174"  jeter3.bam > jeter.svg
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translocation.svg
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