In our lab we have preliminary assembly on non-model genome organism. In the assembled genome, length varies from contig of 500 (shortest) to scaffold of 2000000 bp (longest). I want to to identify SNP with same subset of illumina paired-end reads that were used in genome assembly. Is there any criteria on contig/scaffold length for identifying SNP?. If I have to normalize contig length how I can do it before calling SNP?
Question: Contig/Scaffold Length- Variant Calling
5.4 years ago by
williamjohn360 • 90
williamjohn360 • 90 wrote:
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