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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Need to support complex rearrangements in SV (VCF) #1423

Open yfarjoun opened 5 years ago

yfarjoun commented 5 years ago

The VCF parser is currently unable to parse VCFs with complex rearragnements and this is showing up as Picard issues: https://github.com/broadinstitute/picard/issues/1406

Need to prioritize and fix.

cwhelan commented 5 years ago

Just wanted to alert whoever looks at this that @vruano started to work on this and ended up wanting to refactor the Allele class. A lot of that work is in this large PR:

https://github.com/samtools/htsjdk/pull/1370

There may be a shorter-term fix to prevent errors, but this was his attempt to restructure the allele class so that it could support https://github.com/samtools/htsjdk/issues/18

jrobinso commented 4 years ago

@yfarjoun I also need to support this in IGV, I have no idea what it will do with a complex SV but probably nothing useful. I see this is still open here, when fixed could you provide me with your test cases (VCFs)?

vruano commented 1 year ago

@cwhelan is there still and interest in this?

cwhelan commented 1 year ago

This is definitely something we still need to implement at some point.

vruano commented 1 year ago

In this case I can undust the old large PR code with respect SV allele support and put you as a reviewer, @cwhelan. Do you have some use cases in gatk or gatk-sv that have their own custom Java solutions?