Instructions: This branch is specifically used for Deep Exome Sequencing and Deep Panel TSO500 sequencing requests when collaborators are interested in studying mosaic variants. Please use this branch along with Cre's mosaic-pipeline branch! Key developments:
The crg2 mosaic pipeline generates an exome-wide report for mosaic variants using freebayes mosaic calling parameters. The reports will be stored in “report/freebayes_mosaic/” folder. This report will be generated for all exomes processed in this branch. The freebayes_mosaic caller detects variants at allele fraction (VAF)>5%. For detecting mosaic variants with VAF<5%, we suggest using a gene-panel based approach with GATK Mutect2 caller.
The crg2 mosaic panel pipeline creates a panel report using GATK Mutect2 caller. The panel reports will be stored in “report/gatk_somatic/” folder. Mosaic panel will be kicked off when a <family>_panel.tsv file path is provided in the [run][panel] field inside config.yaml. The panel tsv file consists of one column with column name Gene ID and common gene names in rows.
All positive control sample test runs are located at /hpf/largeprojects/ccmbio/pxu/C4R/test-runs/mosaic-workflow/
Instructions: This branch is specifically used for Deep Exome Sequencing and Deep Panel TSO500 sequencing requests when collaborators are interested in studying mosaic variants. Please use this branch along with Cre's mosaic-pipeline branch! Key developments:
The crg2 mosaic pipeline generates an exome-wide report for mosaic variants using freebayes mosaic calling parameters. The reports will be stored in “report/freebayes_mosaic/” folder. This report will be generated for all exomes processed in this branch. The freebayes_mosaic caller detects variants at allele fraction (VAF)>5%. For detecting mosaic variants with VAF<5%, we suggest using a gene-panel based approach with GATK Mutect2 caller.
The crg2 mosaic panel pipeline creates a panel report using GATK Mutect2 caller. The panel reports will be stored in “report/gatk_somatic/” folder. Mosaic panel will be kicked off when a
<family>_panel.tsvfile path is provided in the[run][panel]field insideconfig.yaml. The panel tsv file consists of one column with column nameGene IDand common gene names in rows.All positive control sample test runs are located at /hpf/largeprojects/ccmbio/pxu/C4R/test-runs/mosaic-workflow/