Output FASTQ donor reads from BAM are all forward direction.

molgenis / VaSeBuilder

Validation Set Builder

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Output FASTQ donor reads from BAM are all forward direction. #85

Closed TDMedina closed 4 years ago

TDMedina commented 4 years ago

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,