Consensus sequence calling with normalisation of indels
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8 days ago

I'm following the workflow suggested by samtools here to produce a fasta with the consensus sequence.

The workflow goes like this:

# call variants
bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Oz -o calls.vcf.gz
bcftools index calls.vcf.gz

# normalize indels
bcftools norm -f reference.fa calls.vcf.gz -Ob -o calls.norm.bcf

# filter adjacent indels within 5bp
bcftools filter --IndelGap 5 calls.norm.bcf -Ob -o calls.norm.flt-indels.bcf

# apply variants to create consensus sequence
cat reference.fa | bcftools consensus calls.vcf.gz > consensus.fa

It's not clear to me if/where/how the calls.norm.flt-indels.bcf file I've made is used by the final bcftools consensus function??

samtools bcftools consensus • 59 views

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