Hello, I would like to test LoFreq pipeline in human germline genome. The NGS data were sequenced by MGI T7 or T10 and aligned with bwa-mem2. What pipeline would recommend? Is it recommended to use trimmed fastq? Can I use "viterbi", "indelqual" and "call-parallel"?
Hello, I would like to test LoFreq pipeline in human germline genome. The NGS data were sequenced by MGI T7 or T10 and aligned with bwa-mem2. What pipeline would recommend? Is it recommended to use trimmed fastq? Can I use "viterbi", "indelqual" and "call-parallel"?