Closed skchronicles closed 5 years ago
mm9 is not supported by the whole genome/exome pipelines. If you look at the mm9.json file, it is actually using mm10 reference files:
mm9.json
{ "references": { "exomeseq": { "BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa", "PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_dbSNP_allStrains_compSet.vcf.gz", "GENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa", "CHROMS": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chrX","chrY","chrM"], "INDELSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz", "KNOWNINDELS": "-known /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz", "KNOWNRECAL": "-knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz", "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz", "KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz", "KNOWNVCF2": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz", "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_genome.nix", "genomeseq": { "BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa", "GENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa", "CHROMS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_chromosomes", "INDELSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz", "KNOWNINDELS": "-known /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz", "KNOWNRECAL": "-knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz", "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz", "KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz", "KNOWNVCF2": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz", "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_genome.nix", "CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/genome.fa", "SNPSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",
Solution: Adding a pop-up box to warning users if they select the wrong reference genome.
Pushed changes to activeDev:
GUI Warning Message: Whole Exome/Genome Pipelines
mm9 is not supported by the whole genome/exome pipelines. If you look at the
mm9.json
file, it is actually using mm10 reference files:Solution: Adding a pop-up box to warning users if they select the wrong reference genome.