Closed mbhall88 closed 4 years ago
In order to create a SNP distance matrix using snp-dists we need fasta sequences for each sample's variant calls in a multi-fasta file.
snp-dists
bcftools consensus does not quite do what we need. It doesn't adhere to FILTER and its behaviour at missing/null sites may not be how we like.
bcftools consensus
@iqbal-lab I know I sound like a broken record, but what base shall we produce in the following circumstance:
bcftools
.
--missing
N
In order to create a SNP distance matrix using
snp-distswe need fasta sequences for each sample's variant calls in a multi-fasta file.bcftools consensusdoes not quite do what we need. It doesn't adhere to FILTER and its behaviour at missing/null sites may not be how we like.@iqbal-lab I know I sound like a broken record, but what base shall we produce in the following circumstance:
bcftoolsoutputs the reference position).(bcftoolsoutput the reference position unless you use the--missingparameter)bcftoolsoutputsN)