Tobias Rausch

This is based on the paired-end distributions and how many pairs support an SV and whether the SV is supported by split-reads.

I think that's a duplicate question with issue [https://github.com/dellytools/delly/issues/385](https://github.com/dellytools/delly/issues/385) so I am closing this one.

Ah sorry, so CIPOS and CIEND are completely derived from the mapping locations of reads and given that germline SVs are often homology-mediated (repeat-mediated) these can be quite misleading. That's...

[Sansa](https://github.com/dellytools/sansa) uses delly's INFO/CONSENSUS sequence which is the ALT sequence + surrounding sequence (i.e., a local assembly of SV supporting reads).

SV and CNV tools use many custom INFO fields in the VCF spec and this makes merging CNVs across tools very difficult. For renaming chromosome names in VCF files, bcftools...

You can simply run `delly cnv` with default options and then plot all chromosomes. For humans, male samples should then show a copy-number of 1 for chrX and females a...

Hi Kun, OpenCV operates on images, which are arrays of pixels so vector formats like SVG would be difficult. You can set, however, the width and height of the plot...

For wally, forward matches are in blue, reverse matches in orange. I haven't used pysam.

Does pysam report relative to the match (just the given SAM record) or relative to the primary alignment?

Can you try this with pysam: ``` echo -e ">ref\nATCTTTGGTGTCTGTGTGTGTGCGCGCGCACGTGCATGTGTGTGAGTTGTCATTGTTTTTGTTTGTTTTG\nTATTCCTCAGAAATAGAAAGCTCCCATTAGG" > ref.fa echo -e ">query\nATCTTTGGTGTCTGTGTGTGTGCGCGCGCACGTGCATGTGTGTGAGTTGTCATTGTTTTTGTTTGTTTTG\nCCTAATGGGAGCTTTCTATTTCTGAGGAATA" > query.fa bwa index ref.fa bwa mem ref.fa query.fa | samtools sort -o query.bam -...