Consensus sequence calling with normalisation of indels
0
0
Entering edit mode
8 days ago

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

https://samtools.github.io/bcftools/howtos/consensus-sequence.html

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
ADD COMMENT

Login before adding your answer.

Traffic: 3078 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6