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
1 answer
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
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.
Strange that it has to be piped, but glad that it worked.
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What's the problem ? Do you have an error ? How do you generated this vcf ? ....
Yes, I got an error, saying failed to open pathto/file.mpileup