mpileup format to vcf

Question

[AGE]

I'm wondering if there's a simple way to convert directly from mpileup format to vcf without having to go through all the steps of creating a bam files to bcf to vcf etc. https://www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_AgriOmics/dan_bolser_snp_calling.pdf

I just want the variable sites from the mpileup file in vcf format.

I tried this and didn't work (Generating Both Pileup And Vcf/Bcf Using Samtools Mpileup)

bcftools view -v -c file.mpileup > file.vcf

[Titus]

What's the problem ? Do you have an error ? How do you generated this vcf ? ....

[AGE]

Yes, I got an error, saying failed to open pathto/file.mpileup

Answer 1

[Kevin Blighe]

I think that you may need bcftools call. The typical way to call variants is to run bcftools mpileup and pipe the output into bcftools call

[AGE]

I tried this:

bcftools call -v -c file.mpileup > file.vcf

Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid Failed to open file.mpileup: unknown file type

[Kevin Blighe]

Can you pipe the pileup into bcftools call? In the description for call, it says:

About:   SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup.
         This command replaces the former "bcftools view" caller. Some of the original
         functionality has been temporarily lost in the process of transition to htslib,
         but will be added back on popular demand. The original calling model can be
         invoked with the -c option.

[AGE]

It worked with the pipe

bcftools mpileup -f genomic.fa file.bam | bcftools call -vm > file_var.vcf

[Kevin Blighe]

Strange that it has to be piped, but glad that it worked.