Closed ghzhaole closed 3 years ago
Hi,
I am not sure exactly what caused the issue given the log, but as a first step, can you double-check if the reference VNTR file (hg38_selected_VNTRs_Illumina.db) is correct?
Hi,
I am not sure exactly what caused the issue given the log, but as a first step, can you double-check if the reference VNTR file (hg38_selected_VNTRs_Illumina.db) is correct?
Thank you for the reply! The reference VNTR file was downloaded from vntr_data_recommended_loci_hg38.zip file. And most of samples can run successfully with the reference VNTR file. Only several of them failed. And if it's convenient, I can provide the failed results to you.
Oh, I missed the part that only several of them failed. Yes, can you please send me the failed results to jonghunpark@ucsd.edu? If possible, one of the bam files that failed would be best for me to figure out the issue as I can reproduce the issue.
Resolved. (Running again fixed the issue)
Hi Mehrdad,
I've installed adVNTR-1.4.1 on Linux, when I running samples in batch, some of them produce the fllowing error:
Here is my command:
advntr genotype -t 2 --alignment_file 6814D.marked.realigned.recal.bam --working_directory 6814D -m hg38_selected_VNTRs_Illumina.db -of vcf -o 6814D_vntr.vcf
Could you please help me figure out what the issue is? Any help is greatly appreciated!