Nils Engel

Hi, I have a problem using lofreq with human sequencing data and hg19 or GRCh38 reference sequences ( downloaded from NCBI with manually changed file extension .fna -> .fa). I guess it might be a problem with improper file format or index. I get an output as follows: nils321$ lofreq checkref GRCh38_latest_genomic.fa 1214474-H8.bam [fai_load] build FASTA index. [fai_fetch_seq] The sequence "1" not found FATAL(samutils.c|checkref:653): Failed to fetch sequence 1 from fasta file Failed An fasta index...