Absolutly All positions in mpileup (previously -aa)
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Feature
- Clarity
- Mostly clear
- Activity status
- Stale
- Domain
- bioinformatics, cli
Research direction
Begin with the bcftools mpileup command and compare its output with samtools mpileup -aa using the attached XMEN example files. Confirm that the requested behavior is a VCF containing every reference position, including sites with no read coverage; done means establishing the supported command or the scope of a needed feature.
Written by the indexing model from the issue text.
Description
Dear developers,
I am looking to generate a VCF file in which all positions of the reference are represented - so also those where my input bam has no read coverage. In SAMtools mpileup, the option -aa exists which does what I need, but I understand SAMtools mpileup is depricated and shouldn't be used (?). I also am unable to pipe the output from SAMtools mpileup into BCFtools call for generating a VCF, have so far been unable to find another way to convert SAMtools' pileup format to a VCF. Is there a native option in BCFtools mpileup that would result the -aa behaviour from SAMtools, ie resulting in a VCF where all bases of the reference are present?
Any suggestions would be much appreciated! I'm attaching a small example file, in case that helps.
XMEN.zip
way to reproduce:
bcftools mpileup XMEN1_10.bam -f XMEN-reference_10.fasta
outputs only sites with coverage
samtools mpileup -aa XMEN1_10.bam
outputs all sites (in pileup format I think?)
Many thanks!
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- Merged PRs (30d)
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