BAM files record all reads with their forward sequences, even if the original sequence was from the reverse strand. Currently, when reading from a BAM file, all reads are being written to FASTQs in the forward direction, causing decreased mapping quality, incorrect insert sizes, etc, and causing validation variants to be missed,
BAM files record all reads with their forward sequences, even if the original sequence was from the reverse strand. Currently, when reading from a BAM file, all reads are being written to FASTQs in the forward direction, causing decreased mapping quality, incorrect insert sizes, etc, and causing validation variants to be missed,