Dear community members,
I face a problem while using Manta - it complains that 2 reads with the same ID exist in the read group.
Existing read: FCC3FB1ACXX:3:2313:16454:24691/2 chrom:pos:strand chr4:84367961:+ cigar: 53M47S templateSize: 53 SA: chr12,68316771,+,48H52M,122,0; mateChrom:pos:strand chr4:84367976:- New read: FCC3FB1ACXX:3:2313:16454:24691/2 chrom:pos:strand chr12:68316771:- cigar: 33S67M templateSize: -67 SA: chr4,84367976,-,38M62H,62,0; mateChrom:pos:strand chr12:68316771:+
I decomposed the BAM file into FASTQs. Run Dragen from fastqs - same failure.
Could you help me, what should I do with my FASTQ files to avoid such reads that have same ID and are assigned to the same read group?
I wrote a script to keep only reads with unique IDs from FASTQs (decomposed from BAMs) - surprisingly there are tons of reads with same IDs and maybe just removal of equal IDs reads is not a strategy which can help.