Question: Contig/Scaffold Length- Variant Calling
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gravatar for williamjohn360
5.4 years ago by
Malaysia
williamjohn36090 wrote:

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?

variant-calling contigs snp • 2.0k views
ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by williamjohn36090
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