Question: Which contigs formed the consensus sequence
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5.2 years ago by
low.weiquan0 wrote:


I am currently carrrying out a SNP calling pipeline and I have forward and reverse read files that used bwa for alignment and then using samtools mpileup to get the contigs in the form of vcf file. I then proceeded to find the consensus sequence by using GATK FastaAlternateReferenceMaker. How do I check which contigs are used in forming the consensus sequence and even the order?

snp alignment • 1.6k views
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