Caleb Lareau
Caleb Lareau
added some notes on the R package install-- thanks for that note @JZL I don't have any direct experience making a conda package but would welcome a pull request from...
My best guess is that the mitochondrial chromosome in the run and what’s in the fasta / bam file are different. I think maegatk assumes chrM and maybe you have...
It says you are getting a memory error when parsing the fasta file; can you supply the fasta that is only the mitochondrial genome (there are some built in already...
> Also, the definition of -mr (minimum reads) was used incorrectly. The function used to call -C in freebayes is actually minimum alternative read, which is not the same thing...
Hi @uqjlu8, your error stems from an improperly specified bam file header: Error in the scatter log (line 83): ``` ERROR::READ_GROUP_NOT_FOUND:Record 1, Read name NS500239:389:H3F5JBGXC:1:12210:7650:20169_GTCACAATCGGATGGA-2+CTGTCACATT, RG ID on SAMRecord not...
just to clarify-- did the test data work OK for you?
Hmmm okay— I don’t see what an obvious solution is here other than trying to manipulate the input bam file header… What is samtools view -H of the input bam...
version 0.1.2 was for indel calling, so I don't think it'll impact anything for you. You can try though-- just clone the repo then install it from the local branch:...
@vincent6liu would you mind commenting here?
I was able to clone the repo and install maegatk-indel via `pip install -e .` for a new version of python: ``` python --version Python 3.11.6 maegatk-indel --help Usage: maegatk-indel...