I have a query regarding consensus sequence assembly where reference bases are replaced with variants with a minimum of 3 read depths, using bcftools using the below command.
bcftools mpileup -f ref.fasta mapped.bam | bcftools call -c | vcfutils.pl vcf2fq -d 3 > cons.fq
Still, if I check the consensus sequence in IGV the variant is not in the consensus sequence at low coverage site.
Even I mapped reads in CDS sequence using "end to end " alignment so I already prohibit soft clipping.
I would like to compare pairwise sequence distance further so every variant is important even if ts low coverage side with a minimum of 3 reads depth.
Is there any parameter I am missing in my above command?
Kindly guide me! Thank you
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written
by
Info.shi •
1 answer
To produce consensus use a different methodology as described here:
https://samtools.github.io/bcftools/bcftools.html#consensus
and also:
https://samtools.github.io/bcftools/howtos/consensus-sequence.html
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