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Hello everyone,
I sequenced some rice genome using HiSeq 2000 with ~100X coverage. I used BWA to do the alignment and want to use Samtools to do SNP calling. Now I have a difficulty to determine the maximum coverage of read depth in Samtools VarFilter script. Should I set the depth to 200 or 500? Thank you very much.
Muhua
I sequenced some rice genome using HiSeq 2000 with ~100X coverage. I used BWA to do the alignment and want to use Samtools to do SNP calling. Now I have a difficulty to determine the maximum coverage of read depth in Samtools VarFilter script. Should I set the depth to 200 or 500? Thank you very much.
Muhua