Dave Larson

icon company The McDonnell Genome Institute at Washington University icon location Saint Louis, MO icon location Bioinformatics https://twitter.com/Ernfrid77

Results 34 comments of Dave Larson

svtools Genotype + Key Error: 'END'

Your input VCF must have an END tag in the VCF for svtyper to work. If your input file is from `svtools merge` then I'd expect it to exist.

"Parameter required for id", resolved by manually inserting id fields in `-sr` arguments

Can you attach a copy of the header of your BAM and provide the output from running lumpyexpress with the -v option on?

cromwell 35 errors out on workflow

Hi Kaushik, Send my regards to Devin! We've only recently updated to Cromwell 34, but I have noticed some incompatibilities with some of our old workflows. I must also admit...

hexdump is missing from lumpy container

@indraniel - it was, but sambamba has a bug to do with CRAM so I believe we're using samtools which auto-detects if it's CRAM or BAM.