I am stuck with this issue and could not find a solution on the many posts which have already been written on it.
After mapping with bwa mem (same when trying bwa aln on the same fastqs), I validate my bam files with picardtools ValidateSamFile and I got about 3% of the reads marked by a MATE_NOT_FOUND error. Already tried:
- Fastq reads 1 and 2 are in sync.
- Running FixMateInformation did not fix it.
- Sorting the bam did not fix it
- Checking the flag of these problematic reads in the bam, I could see that most of them are already flagged as "mate unmapped" (then why validateSam complains?) and only some of them are flagged as both mates are mapped.
Should I simply not care about it and go on with the downstream SNP calling (I will use FreeBayes)?
Any idea to solve or understand this issue will be very appreciated.
All the best, Emiliano