Which contigs formed the consensus sequence · Biostar

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Which contigs formed the consensus sequence

Hi,

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 snp alignment

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written 11.2 years ago by low.weiquan •

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