Does anyone know if the tool vcf-consensus supports indels insertion in the consensus sequence?
It supports only SNVs and deletions. Not insertions
Not sure about vcftools-consensus but indels are taken into account with "bcftools consensus" and is probably faster than vcftools:
bcftools consensus --fasta-ref <reference.fasta> <file.vcf.b.gz> --sample <IND> -o <output_consensus.fasta>
See docs: https://samtools.github.io/bcftools/bcftools.html
For some reason when I try bcf consensus, indels are not taken into account.
When i do samtools mpileup and bcftools call to create a vcf file, it will annotate indels but with a 0/0 genotype.
I think that has to do with bcftools consensus not including indels it in the consensus seq.
Have you noticed this before?
This is my pipeline:
bbmap.sh index ref.fasta
bbmap.sh ref='ref.fasta' in='sample.fasta' out='output.sam'
samtools view -bS output.sam > output.bam
samtools sort output.bam > sorted.bam
samtools index sorted.bam
samtools mpileup -uf SA05sequence.fasta sorted.bam | bcftools call -c > vars.vcf
bgzip -c vars.vcf vars.vcf.gz
tabix -p vcf vars.vcf.gz
bcftools consensus --fasta-ref ref.fasta vars.vcf.gz -o consensus.fasta
Sorry guys, I figured it out.
My problem was caused by the difference of indel representing by BBMap.
I now call BBMap using sam=1.3 and for bcftools I use call -m (multiallelic)
Figured it out using: http://seqanswers.com/forums/showthread.php?t=61535
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