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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
GNU General Public License v3.0
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ont2d not supported by bwa #108

Open afadda1 opened 9 months ago

afadda1 commented 9 months ago

Hi, it seems like bwa mem does not support ont2d reads /BWA/0.7.7/bwa mem -t1 -x ont2d -M -a /gpfs/software/genomics/HLA-LA_comp/HLA-LA/src/../graphs/PRG_MHC_GRCh38_withIMGT/extendedReferenceGenome/extendedReferenceGenome.fa /R_U.fastq.splitLongReads | /gpfs/software/genomics/SAMtools/1.9/bin/samtools view -@ 0 -Sb - > /PRG38/SIR000174000075/remapped_with_a.bam.unsorted mem: invalid option -- 'x'