When mapping reads with bwa mem, if you use the -M flag, the split reads are maked as secondary and they will not be used by smoove to get split-read support. This will cause all the variants in your VCF file to have SR=0. If you don’t use split-read support... [Read More]

The pipeline to map the reads from several samples to a (reference) genome is now available. As input it takes a .fasta file of a reference genome, and one or more paths to directories that contain reads. The pipeline will go through every subdirectory of the path you gave as... [Read More]

The pipeline to perform structural variant calling in a population using Smoove is now available. It also runs VEP and performs PCA. You can find the description here. There you can also find the tools that the pipeline uses and the output. The pipeline can be found here. [Read More]

In this post I will show how to solve some Smoove issues I came across. I’m using smoove v0.2.8 installed with conda. [Read More]

The pipeline for mapping short reads and performing variant calling is now available. You can find a short description here. There you can also find the tools that the pipeline uses and the output. The pipeline can be found here. [Read More]