---
# System prepended metadata

title: Breakout session
tags: [Twist_DNA_Solid]

---

---
tags: Twist_DNA_Solid
---

# Breakout session

**Date: 31/3 2022**

## CNV
**Calling programs**
CNVkit and GATK_CNV are used in the current pipeline. Manta for larger INDELs? 
BND: 5000 overlap 70% / 80 % in merging and 80% in testing
Artifact DB: minimum 30-40 samples
Use everything and annotate in locusdb to select real regions
Delly, play around of number split reads and Brass?

**Tools to merge calls**
No other good solutions -> SVDB

**Merging criteria** 
Union / Intersect? Overlap % (reciprocal overlap)?
Not applicable for svdb, more important to look att overlap

**Filtering**
Filtering based on normals only? Min size criteria? SVDB? Overlap?
How to use the BAF in filtering? 
How to handle copy neutral calls? no good way of handle it
Only report clinically relevant genes? (TSO500 gene list for amplifications, LoH gene list)
Calling criteria? (6X for amplifications, 0-1X for LoH dependent on region, 1X for chromosome arm LoH).
Should be solved by artifacts databases 

**CNV visualization tools**
[gens](https://github.com/Clinical-Genomics-Lund/gens)



## Child cancer (cc) WGS


**What is in production**
In Uppsala Martin Rippin is working on building this based on hydra snakemake. Uppsala does tumour-normal at the moment and are planning to start to use tumour only. For Uppsala the hopeful plan is to start using SCOUT cancer in the clinic.

In Göteborg they have a WGS cc pipeline built in snakemake but they are planning to switch to hydra.

In Lund they have a nextflow pipeline in production and are not currently planning to switch to snakemake.

Stockholm has [Balsamiq](https://github.com/balsamiq) which is in production and they are unsure if they have resources to switch to hydra

(We send currently our samples to Göteborg for sequencing and downstream analysis but in the future will be sending to Stockholm)

**Heavy computation problem**
- Lund uses Sentieon
- Uppsala uses parabricks: modules for alignment and variant calling
- Göteborg uses Sentieon

**Current status in hydra**
CNV module is not optimised and doesn't have a version tag yet
In hydra wgs cc what is lacking is integration to what clinicians need
- one possible way could be to use [gens](https://github.com/Clinical-Genomics-Lund/gens)

**Future steps**
- Hopefully gain inspiration to hydra from [Balsamiq](https://github.com/balsamiq) and what Göteborg has in production
- Add modules to hydra which are going to be actually used in the future
- Gather a wishlist of modules to include

**Tool tips**

- [Petagene](https://www.petagene.com/) (proprietary) for fastq and bam compression
- Crumble: [blog post](https://blog.dnanexus.com/2018-07-23-breaking-down-crumble/), [Github](https://github.com/jkbonfield/crumble) for bam/cram compression (can even improve variant-calling accuracy)
- [Spring](https://github.com/shubhamchandak94/Spring) fastq compression




