I have read various threads here that suggested that the "Parse error reading exome.fasta.amb" is due to the whitespaces in my reference file hg19.fa
Basically, I run and get $ bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
BWA error [bns_restore_core] Parse error reading ref.fa.amb
I think I have removed whitespaces using:
tr -d ' ' < in.fa >out.fa ## remove all spaces
also tried without success: sed 's/ *$//g' in.fasta > out.fasta
I am trying to align/map exome.fastq to indexed hg19(ref.fa). I have read that bwa mem have issues with whitespaces but I am stuck here. Did anyone have the same issue and got it solved? Is there a workaround? Thanks.