Hi all
I have a few genomes sequenced using illumina. I have used samtools and vcfutils to make a consensus for each. All pretty standard stuff. However using vctutils to make the consensus gives me far to many N nucleotides to be happy with.
Is there a way that i can create this consensus but where it currently has provided an N nucleotide it actually inserts the reference nucleotide in its place?
Your help would be much appreciated. Any ideas?
I have a few genomes sequenced using illumina. I have used samtools and vcfutils to make a consensus for each. All pretty standard stuff. However using vctutils to make the consensus gives me far to many N nucleotides to be happy with.
Is there a way that i can create this consensus but where it currently has provided an N nucleotide it actually inserts the reference nucleotide in its place?
Your help would be much appreciated. Any ideas?
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