I encountered an issue with the AS reads being all zero for a single end bam file, and realized all reads were filtered out by this filter. My understanding is that only properly paired reads will have an "=" sign in column 7, so this filter throws out all single end reads which are marked by "*" in column 7. I feel like this line of filter should be modified for single end mode. Additionally, if the number of reads in the bam file is zero or if AS reads are alarmingly low, a warning could be shown.
https://github.com/natsuhiko/rasqual/blob/5aa553cf1b6501cf7ecd61a5efb34f7f20d354c6/src/ASVCF/createASVCF.sh#L121C15-L121C35
I encountered an issue with the AS reads being all zero for a single end bam file, and realized all reads were filtered out by this filter. My understanding is that only properly paired reads will have an "=" sign in column 7, so this filter throws out all single end reads which are marked by "*" in column 7. I feel like this line of filter should be modified for single end mode. Additionally, if the number of reads in the bam file is zero or if AS reads are alarmingly low, a warning could be shown.