I used bwa to align paired-end reads to a reference. I'm trying to convert the SAM file to a BAM file, but am getting the following error:
[E::sam_parse1] SEQ and QUAL are of different length
[W::sam_read1] parse error at line 25199
[main_samview] truncated file.
It seems the qual line is split on two different lines. I had previous error before this one for line 25197. I found the sequence in the fastq's and the qual line started with 3 '@' symbols for read 1. I removed sequence from both fastq files and it appears there are other offending sequences. The qual and sequence line in the fastq's are the same length, but in the sam file they are not.
This is the sequence from read 1 fastq:
This is the sequence from read 2 fastq: