filtered.bcf file much larger than raw.bcf file

Question

[PKSWEE11]

After using mPileup (Sam Tools v. 1.6) I get files that are in the neighborhood of 12 GB. Next, I use Bcftools filter (bcftools v. 1.6) to filter out variants with read depth less than 2 or greater than 100. The filtered files are around 85 GB! Why are the filtered files so much larger? After all I am filtering out sequence right? Here's the bcftools filter script

bcftools filter --threads 20 raw.bcf -e 'DP<2 || DP>100' > filtered.bcf

Any thoughts would be appreciated. Thanks

Answer 1

[Pierre Lindenbaum]

your generating a VCF file (plain text), not a binary (small) BCF.

see options:

-o, --output <file>           write output to a file [standard output]
-O, --output-type <b|u|z|v>   b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]

[PKSWEE11]

Thanks! That was very helpful