Should indel calling allowed without indel quals?

andreas-wilm / lofreq3

LoFreq Version 3

MIT License

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Should indel calling allowed without indel quals? #37

Open andreas-wilm opened 3 years ago

andreas-wilm commented 3 years ago

Base qualities are always present as per SAM standard. For indels they might be missing. LoFreq currently happily calls indels with missing quals, which should probably only be possible when scientifically requested