Hello,
I'd like to filter for sites that have a DP>5 in my normal sample and DP>10 in the tumor. My vcf has two samples columns, TUMOR NORMAL. How do I do that with a bcftools expression? I see in the documentation how to apply the filter for one or all samples in a vcf row but I couldn't find a way to specify the sample name.
Thanks a lot.
Hava a look at SnpSift filter. 

With SnpSift  you can build any expression that evaluates to TRUE / FALSE using the attributes of the variant and or the attributes of one or more specific samples. 

http://snpeff.sourceforge.net/SnpSift.html#filter

    cat my.vcf | java -jar SnpSift.jar filter "GEN[0].DP > 5 && GEN[1].DP > 10"