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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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Bcftools mpileup #2237

Open Mashindersingh opened 3 months ago

Mashindersingh commented 3 months ago

I am using 91 bam files each of 500 mb size Bam files sorted and indexed and reference maize genome is also indexed of 2.5 gb . Then i proceeded for bcftools mpileup for bcf file but the command is running from 2 days and file is growing to 1.5 tb So to estimate size if bcf or i want to to know this file size is fine or unusal or is there any error

pd3 commented 3 months ago

I am using 91 bam files each of 500 mb size Bam files sorted and indexed and reference maize genome is also indexed of 2.5 gb . Then i proceeded for bcftools mpileup for bcf file but the command is running from 2 days and file is growing to 1.5 tb So to estimate size if bcf or i want to to know this file size is fine or unusal or is there any error

This looks like a bug of some kind. You can try with a single bam and extrapolate to the 91 bams. Make sure you are running the latest version. What is the exact command you are running? If the data is long reads, are you running with some of the -X presets?