Minimum Information about Whole-genome Sequencing

Sydney-Informatics-Hub / Fastq-to-BAM

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

GNU General Public License v3.0

20 stars 7 forks source link

Minimum Information about Whole-genome Sequencing #27

Closed DarioS closed 4 days ago

DarioS commented 1 week ago

Some journals now require detailed metrics, e.g. International Journal of Cancer. This pipeline does not calculate most metrics.

calizilla commented 4 days ago

Hi Dario, the pipeline doesn't claim to calculate these metrics and there are many external tools that can be run to obtain the details this journal is asking for. For example you could try this workflow, to be run after the BAM creation: https://github.com/Sydney-Informatics-Hub/bamQC-nf

We are not actively updating this pipeline as newer tools bwa-mem2, DeepVariant and GLNexus provide better efficiency and sensitivity than the GATK pipeline.

DarioS commented 4 days ago

Indeed, bamQC-nf calculates all five columns of the template table. Thanks for alerting me to it.