We’re using the standard SAMtools SNP calling protocol (samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf) to look for sequence variants in bacterial genomes.
I’m really new to this, but it sounds like the protocol is geared towards diploid organisms by default. I hoping someone might know if there’s anything that should be changed to use it on haploid genomes? The –s or –p options in SAMtools mpileup look like they might be useful, but I’ve no feel for how to apply them correctly for this. Any help would be really appreciated!
I’m really new to this, but it sounds like the protocol is geared towards diploid organisms by default. I hoping someone might know if there’s anything that should be changed to use it on haploid genomes? The –s or –p options in SAMtools mpileup look like they might be useful, but I’ve no feel for how to apply them correctly for this. Any help would be really appreciated!
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