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I'm using ivar consensus to create updated reference sequences in simple cases (i.e. mapping of Sanger contigs to a reference assembly), similar to FastaAlternateReferenceMaker. For this to work, consensus should take reference residues at positions with low (zero) coverage, an option that AFAICT it does not have.
$ cat pile.txt
ref 1 A 0 * *
ref 2 A 1 T ~
ref 3 T 0 * *
ref 4 G 0 * *
ref 5 G 0 * *
$ ivar consensus -p cons -m 1 < pile.txt
Minimum Quality: 20
Threshold: 0
Minimum depth: 1
Regions with depth less than minimum depth covered by: N
Reference length: 5
Positions with 0 depth: 4
Positions with depth below 1: 4
$ cat cons.fa
>Consensus_cons_threshold_0_quality_20
NTNNN
A workaround is to mess with the pileup, forcing zero-depth positions to have the reference residue:
$ awk '!$4{$4=1;$5=".";$6="~"}1' OFS=\\t pile.txt | ivar consensus -p cons -m 1
Minimum Quality: 20
Threshold: 0
Minimum depth: 1
Regions with depth less than minimum depth covered by: N
Reference length: 5
Positions with 0 depth: 0
Positions with depth below 1: 0
$ cat cons.fa
>Consensus_cons_threshold_0_quality_20
ATTGG
But I think it would be natural to add an argument (or to extend -n) that would indicate that the reference should be called for regions with zero coverage (perhaps in lower case).
The text was updated successfully, but these errors were encountered:
I'm using
ivar consensus
to create updated reference sequences in simple cases (i.e. mapping of Sanger contigs to a reference assembly), similar to FastaAlternateReferenceMaker. For this to work, consensus should take reference residues at positions with low (zero) coverage, an option that AFAICT it does not have.A workaround is to mess with the pileup, forcing zero-depth positions to have the reference residue:
But I think it would be natural to add an argument (or to extend
-n
) that would indicate that the reference should be called for regions with zero coverage (perhaps in lower case).The text was updated successfully, but these errors were encountered: