We use revertsam and samtofastq for input bam since fastq files required for shiftfasta tool for circular refs. However, using the reverted fastqs for the non-shifted fasta causes us to lose some reads and hence lose some variants. The fix here is to skip the revertsam and samtofastq for the unshifted fasta when the input is bam file.
We use revertsam and samtofastq for input bam since fastq files required for shiftfasta tool for circular refs. However, using the reverted fastqs for the non-shifted fasta causes us to lose some reads and hence lose some variants. The fix here is to skip the revertsam and samtofastq for the unshifted fasta when the input is bam file.