Hi! I'm using Samtools version 1.3.1. I was analysing some illumina paired-end sequenced samples and I realised that when running mpileup with this version, by default, samtools discards all the Minus Strand reads when there are overlapping reads. Is there any reason why always discards Minus Strand reads? Does it make sense? What happens is that I have some real SNPs in regions where all the reads overlap so, when it discards all the Minus Strand reads, the SNPs appear only in one strand and then it doesn't pass the downstream filters that we apply. I know that with the option --ignore-overlaps I can keep all the overlapping reads so my question is Why samtools does not discard Positive strands or Minus Strands in a random way by default?
Thanks for your attention, Carla
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