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@Sheila Thanks for the info will do!
FYI, problem solved. I've tried add indexFile (.fai) without luck. Turn out it will need all other indexfiles (.bwt,.sa,.pac,.amb,.ann ) as well. Hope it helps for others.
@dannykwells Can you share what you did to solve the third problem? We've faced the same problem when running bwa in command line working but in wdl gave "[E::bwa_idx_load_from_disk] fail to locate the index files" Error. Thanks.
Have the same problem from my wdl. I can run my bwa command in terminal without any problem. bwa mem -m -r /home/cytolab/Software/bwa/hg19.fa /home/cytolab/Software/bwa/1.fastq /home/cytolab/Software/bwa/2.fastq But when i trying to run wdl it g…
@Sheila Thanks! When we do variants interpretation each sample is viewed independently, is there any advantage for keeping the joint genotyping? Will do VQSR after we got more than 30 samples. Best, Wenfu
Just a quick question about joint genotyping. We're doing WES trying to find germline mutations. In each run we will have about 6 samples, they are independent, does not share any phenotype. For my understanding joint genotyping is for the purpos…