Enforcing filter criteria on _all_ samples.

[arq5x]

The following works:

bcftools view -Ou -s 1805 trio.trim.vep.bcf | \
    bcftools view -i 'FORMAT/GT=="1/1"' | \
    grep -v ^# | \
    head -3 | cut -f 10
1/1:0,6:6:18.05:207,18,0
1/1:0,35:35:99:1268,102,0
1/1:15,88:104:99:2850,265,0

But when extracting multiple samples, the condition seems to be an OR:

bcftools view -Ou -s 1805,4805 trio.trim.vep.bcf | \
    bcftools view -i 'FORMAT/GT="1/1"' | \
    grep -v ^# | \
    head -3 | cut -f 10,11
1/1:0,6:6:18.05:207,18,0    ./.:.:.:.:.
1/1:0,35:35:99:1268,102,0   1/1:0,1:1:3.01:38,3,0
1/1:15,88:104:99:2850,265,0 0/1:114,107:224:99:2688,0,2507

How do I enforce AND logic such that the only variants returned are those where both samples are homozygous alternate?

[mcshane]

Looks like no AND logic yet. Have to think how to express that. But for specific case you have, could do:

bcftools view -c4 -s 1805,4805 trio.trim.vep.bcf

[pd3]

I fixed a bug and modified the code (samtools/bcftools@cc5b9d7) so that the following expression should effectively function as AND logic:

bcftools -e 'GT != "1/1"'

[arq5x]

That's great, thanks. In my opinion, I think you ultimately want the ability to enforce that any, all, none, or some (i.e., count >= X) of the samples meet the criteria. This is the logic we allow in GEMINI and it proves to be quite powerful:
http://gemini.readthedocs.org/en/latest/content/querying.html#selecting-sample-genotypes-based-on-wildcards

[pd3]

You are right, that would be nice to support. I'll leave this issue open as a reminder.