Do you know how to get CNVs out of WES data sorted.bam files? (Free)

• gatk4-genome-processing-pipeline-azure

  4 7 0.0 wdl

  Workflows used for processing whole genome sequence data + germline variant calling.

  

The GATK suite is pretty standard for calling germline mutations. Somatic mutation calling is a lot newer/trickier, so I'm just going to link to the GDC's practices.

• sv-callers

  1 70 2.9 Python

  Snakemake-based workflow for detecting structural variants in genomic data

  

Generally, you have multiple ways to tackle this kind of a problem. For short read sequencing you have two types of CNV detection - readdepth based and paired-end based. CNVpytor (CNVnator) for example, is the former. You also have manta and lumpy. A lot of good pipelines use more than one SV caller and integrate them. For example: https://github.com/GooglingTheCancerGenome/sv-callers

• WorkOS

  workos.com sponsored

  The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.

  

Suggest a related project