mapping reads to consensus - O coverage regions
Hi, I performed reference based assembly of bacterial genome as followed: bwa-mem2 mapping reads to reference > marked duplicates with picard > variant calling with freebayes (-H 1) > filtered vcf based on DP>5 and VAF>0.5 with vcffilter > normalized indels with bcftools norm > bcftools consensus -H 1 with filtered and normalized vcf > mapping reads to consensus > polishing with pilon.
Then I calculated coverage samtools depth -d 0 -a based on reads mapped to consensus, and when I inspected coverage per base there are bases with 0 and other low coverage (1-5) bases. Why?
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If you are open to trying an alternate way then perhaps check out this answer by @Brian --> What is the correct procedure to generate a consensus bacterial sequence?
Did you inspect the alignment right after
bwastep? Perhaps your genome is different from the reference used and thus the 0 coverage bases are there to begin with.Hi GenoMax , whole reference is uniformly covered by reads with small SNV/ins/del. Below is the region that is included into consensus but not covered by reads.