(Sanity check) Too many SNPs?

Question

[rightmirem]

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' ./<filename>.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 1

[pfs]

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.