Dear All,
I've used (what I think are) default settings to align paired end Illumina data using bwa then samtools and finishing with mpileup.
Before obtaining my sequences I PCR'd all our strains in a specific area of the genome to confirm their family according to the presence or absence of certain SNP's.
The problem is that the consensus fasta that is derived from mpileup always has the family of the reference strain and not the query strains that I've lined up (despite having good coverage in the region that defines the family).
Somehow the reference sequence is being output rather than the query sequence at this part of the genome.
Can anybody help?
Best wishes and thanks
I've used (what I think are) default settings to align paired end Illumina data using bwa then samtools and finishing with mpileup.
Before obtaining my sequences I PCR'd all our strains in a specific area of the genome to confirm their family according to the presence or absence of certain SNP's.
The problem is that the consensus fasta that is derived from mpileup always has the family of the reference strain and not the query strains that I've lined up (despite having good coverage in the region that defines the family).
Somehow the reference sequence is being output rather than the query sequence at this part of the genome.
Can anybody help?
Best wishes and thanks
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