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

Question

[mhmtgenc85]

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?

Answer 1

[Shane McCarthy]

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

[mhmtgenc85]

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