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BCF file is too big? (from 3,73 GB sorted.bam file to over 200 GB BCF)

I Have a sorted BAM file which is 3,73 GB in size and I use this command;

$ samtools mpileup -u -f wholegenome.fa oz.sorted.bam > oz.bcf

and having a BCF file which is over 200 GB and going file. Is it normal?

alignment next-gen snp
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updated by Shane McCarthy Shane McCarthy • written by Clark_BioMorgan • Clark_BioMorgan

1 answer

The -u flag means you are writing out uncompressed BCF. Use -g instead to write out compressed BCF.

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written by Shane McCarthy Shane McCarthy

tthanks for tthe reply and what would be the size of vcf file generated from 200 GB bcf file?

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written by Clark_BioMorgan • Clark_BioMorgan

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