This branch is based on @pamelaxu213's original mosaic branch. Please test this branch along with cre's mcouse/mosaic branch.
The crg2 mosaic pipeline generates an exome-wide report for mosaic variants using GATK Mutect2. The reports will be stored in the “report/gatk_somatic/” folder. This report will be generated for all exomes processed in this branch. Mutect2 can detect variants with allele fractions as low as ~3% with sufficient depth of coverage. Note that I have added the gnomad allele frequency resource as an argument to Mutect2; this allows the caller to predict if a variant is germline based on its allele frequency in the population, and filter it out.
Mutect2 does not perform joint-genotyping, so we merge individual VCFs using bcftools merge.
All positive control sample test runs are located at /hpf/largeprojects/ccmbio/mcouse/C4R/development/test_mosaic_exomewide/
This branch is based on @pamelaxu213's original mosaic branch. Please test this branch along with cre's mcouse/mosaic branch.
The crg2 mosaic pipeline generates an exome-wide report for mosaic variants using GATK Mutect2. The reports will be stored in the “report/gatk_somatic/” folder. This report will be generated for all exomes processed in this branch. Mutect2 can detect variants with allele fractions as low as ~3% with sufficient depth of coverage. Note that I have added the gnomad allele frequency resource as an argument to Mutect2; this allows the caller to predict if a variant is germline based on its allele frequency in the population, and filter it out.
Mutect2 does not perform joint-genotyping, so we merge individual VCFs using bcftools merge.
All positive control sample test runs are located at /hpf/largeprojects/ccmbio/mcouse/C4R/development/test_mosaic_exomewide/