Question: I have an amalgamated BCF file, containing the variant calls from the FULL GENOME of 70 individuals.

I've run the command ...

bcftools view -i 'TYPE="snp" && AC=140 && GT="hom" && QUAL>20' ./.bcf | wc -l

This should (and based on the output lines I've looked at - does) respond with any variant calls that are SNPs (only), with only one ALT, where the GT is 1/1 for ALL samples. In other words, every sample (out of 70) has this SNP, in both alleles.

The count I got was 30704...meaning there are 30704 different SNPs that every patient shares.

This seems...unlikely. Is this reasonable?

SAMPLE OUTPUT:

1 792862 . C G 228 PASS VDB=0.413797;SGB=-0.693147;MQSB=0.362809;MQ0F=0;MQ=52;RPB=1;MQB=1;BQB=1;DP=5464;DP4=0,1,2859,2288;AN=140;AC=140 GT:PL 1/1:255,144,0 1/1:255,244,0 1/1:255,129,0 1/1:255,175,0 1/1:255,229,0 1/1:255,235,0 1/1:255,255,0 1/1:255,211,0 1/1:255,255,0 1/1:86,9,0 1/1:255,214,0 1/1:255,223,0 1/1:255,220,0 1/1:255,211,0 1/1:255,205,0 1/1:255,232,0 1/1:255,226,0 1/1:255,157,0 1/1:255,220,0 1/1:255,255,0 1/1:255,255,0 1/1:255,87,0 1/1:255,211,0 1/1:255,247,0 1/1:255,223,0 1/1:255,166,0 1/1:255,220,0 1/1:255,223,0 1/1:255,190,0 1/1:255,172,0 1/1:255,226,0 1/1:255,255,0 1/1:255,255,0 1/1:255,241,0 1/1:255,255,0 1/1:255,255,0 1/1:255,238,0 1/1:255,202,0 1/1:255,138,0 1/1:255,196,0 1/1:255,111,0 1/1:255,226,0 1/1:255,255,0 1/1:255,255,0 1/1:255,255,0 1/1:255,208,0 1/1:255,196,0 1/1:255,250,0 1/1:255,226,0 1/1:255,255,0 1/1:255,255,0 1/1:255,235,0 1/1:255,199,0 1/1:255,255,0 1/1:255,157,0 1/1:255,181,0 1/1:255,220,0 1/1:255,163,0 1/1:255,169,0 1/1:255,255,0 1/1:255,255,0 1/1:161,15,0 1/1:255,255,0 1/1:255,255,0 1/1:255,187,0 1/1:255,190,0 1/1:255,255,0 1/1:255,193,0 1/1:255,255,0 1/1:255,126,0

1 822944 . T C 228 PASS VDB=0.978422;SGB=-0.693147;MQSB=1;MQ0F=0;MQ=60;RPB=1;MQB=1;BQB=1;DP=4660;DP4=1,2,2178,2254;AN=140;AC=140 GT:PL 1/1:255,135,0 1/1:255,181,0 1/1:255,90,0 1/1:255,220,0 1/1:255,114,0 1/1:255,169,0 1/1:255,187,0 1/1:255,129,0 1/1:255,144,0 1/1:61,6,0 1/1:255,232,0 1/1:255,160,0 1/1:255,193,0 1/1:255,247,0 1/1:255,169,0 1/1:255,247,0 1/1:255,151,0 1/1:255,99,0 1/1:255,255,0 1/1:255,255,0 1/1:255,255,0 1/1:255,57,0 1/1:255,177,0 1/1:255,250,0 1/1:255,255,0 1/1:255,105,0 1/1:255,220,0 1/1:255,255,0 1/1:255,163,0 1/1:255,169,0 1/1:255,172,0 1/1:255,144,0 1/1:255,255,0 1/1:255,172,0 1/1:255,255,0 1/1:255,235,0 1/1:255,196,0 1/1:255,202,0 1/1:255,190,0 1/1:255,211,0 1/1:255,66,0 1/1:255,214,0 1/1:255,232,0 1/1:255,190,0 1/1:255,123,0 1/1:255,157,0 1/1:255,144,0 1/1:255,178,0 1/1:255,255,0 1/1:255,247,0 1/1:255,255,0 1/1:255,253,0 1/1:255,220,0 1/1:255,250,0 1/1:255,175,0 1/1:255,175,0 1/1:255,132,0 1/1:255,166,0 1/1:255,229,0 1/1:255,255,0 1/1:255,255,0 1/1:55,6,0 1/1:255,169,0 1/1:255,255,0 1/1:255,229,0 1/1:255,157,0 1/1:255,184,0 1/1:255,108,0 1/1:255,241,0 1/1:255,120,0

1 839356 . A C 228 PASS VDB=0.209904;SGB=-0.692976;MQSB=1;MQ0F=0;MQ=60;RPB=1;MQB=1;BQB=1;DP=2889;DP4=1,0,1441,1171;AN=140;AC=140 GT:PL 1/1:255,78,0 1/1:255,66,0 1/1:255,39,0 1/1:255,141,0 1/1:255,151,0 1/1:255,138,0 1/1:255,102,0 1/1:255,69,0 1/1:255,84,0 1/1:65,6,0 1/1:255,120,0 1/1:255,87,0 1/1:255,81,0 1/1:255,117,0 1/1:255,90,0 1/1:255,129,0 1/1:255,129,0 1/1:255,102,0 1/1:255,126,0 1/1:255,123,0 1/1:255,96,0 1/1:255,69,0 1/1:255,169,0 1/1:255,153,0 1/1:255,144,0 1/1:255,90,0 1/1:255,96,0 1/1:255,141,0 1/1:255,111,0 1/1:255,87,0 1/1:255,105,0 1/1:255,102,0 1/1:255,160,0 1/1:255,117,0 1/1:255,141,0 1/1:255,135,0 1/1:255,96,0 1/1:255,157,0 1/1:255,117,0 1/1:255,111,0 1/1:255,78,0 1/1:255,111,0 1/1:255,144,0 1/1:255,102,0 1/1:255,42,0 1/1:255,117,0 1/1:255,69,0 1/1:255,135,0 1/1:255,129,0 1/1:255,129,0 1/1:255,141,0 1/1:255,99,0 1/1:255,126,0 1/1:255,123,0 1/1:255,117,0 1/1:255,111,0 1/1:255,151,0 1/1:255,172,0 1/1:255,132,0 1/1:255,135,0 1/1:255,126,0 1/1:83,9,0 1/1:255,111,0 1/1:255,187,0 1/1:255,111,0 1/1:255,99,0 1/1:255,108,0 1/1:255,72,0 1/1:255,138,0 1/1:255,126,0

Answer: The ALT and REF SNPs do not always correspond to the Major/Minor allele at a SNP position. Thus, in some cases the major allele = ALT allele. This could be driving the numbers you are seeing. The other thing that could be driving these numbers is if al 70 patients are of similar ethnicity. I would recommend looking at the raw reads for a handful of patients at a handful oh these 1/1 SNPs and confirming the SNP characterization.