bcftools consensus files only has reference sequence in it
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Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Domain
- bioinformatics
Research direction
Start by inspecting species1.calls.vcf.gz produced by the samtools mpileup and bcftools call pipeline, then compare it with ref_geneA.fa and the bcftools consensus command. Done means the cause of the reference-only output is established and the expected consensus behavior is documented or reproducible.
Written by the indexing model from the issue text.
Description
After running bwa index on my ref_geneA.fa file and running bwa mem on the ref and different species exome data, I then used samtools to sort and index the output files. I am now trying to get just the consensus sequence from the aln.sorted.bam files for each species, 1 at a time (so I can later align them all using MAFFT to create one MSA).
Here is my command that I am stuck on (the versions of samtools and bcftools are both 1.9).
samtools mpileup -uf ref_geneA.fa species1.aln.sorted.bam | bcftools call -mv -Oz -o species1.calls.vcf.gz
tabix species1.calls.vcf.gz
cat ref_geneA.fa | bcftools consensus species1.calls.vcf.gz > consensus.fa
When I open the consensus.fa it only has the sequence from ref_geneA.fa, and nothing else. Why is this happening?
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
Contributor guide
First steps
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