-
working directory: `/gscmnt/gc2547/griffithlab/yafeng/PRAD`
command: `pvacfuse run --net-chop-method cterm --netmhc-stab --iedb-install-directory /gscmnt/gc2502/griffithlab/yafeng -e 8,9,10,11 TCGA…
-
Hi,
I need some help to understand why CallDuplexConsensusReads did not emit any consensus reads.
fgbio CallDuplexConsensusReads --input=$grouped_bam --output=$concensus_unmapped_bam --error…
-
hello, when i run the sample data , the commad as follows: pyhton MuPeXI.py -v home/jm/mupexi/data/example.vcf -a HLA-A01:01 -e expression.tsv -l 9 -c home/jm/mupexi/config.ini -o home/jm/mupexi/data/…
-
Hi.
I've run pvacseq previously for a test and it wen't ok. Now I'm trying to do it for good but there is something that I'm not being able to understand.
By default I've python 2.7, so I use co…
-
See https://github.com/antigenomics/vdjdb-db/issues/251 by @dmstandley
-
In on some samples (it works on others) the python script failed with this error:
File "MuPeXI.py", line 79, in main
peptide_info, peptide_counters, fasta_printout, pepmatch_file_names = pep…
-
Hi @ruchim I am attempting to run the WDL workflow with Cromwell 30.1 using the following command:
java -jar ~/.dockstore/libraries/cromwell-30.1.jar run /home/ubuntu/topmed-workflows/functional-equiv…
-
Hi.
TIDDIT is running fine for me on GRCh37 bams, but I'm running into a problem with GRCh38.
I'm getting a reference mismatch error, here are the last few lines of output and the error:
working …
-
Hi guys,
Wildtype and Downstream plugins not able to annotated GATK indels vcf file. Amino acid sequences were not generated in VEP processing. Do i need to change any parameter here?
-
I came across some notes I made 20170901, while developing the Helsinki Mutect2 tutorial, to report a particular bug, that I am just now getting around to. Here is the command I ended up using to solv…