Question: (Sanity check) Too many SNPs?
1
gravatar for rightmirem
12 months ago by
rightmirem50
rightmirem50 wrote:

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
variant next-gen filter • 496 views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 12 months ago by rightmirem50
5
gravatar for pfs
12 months ago by
pfs250
USA/Boston
pfs250 wrote:

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.

ADD COMMENTlink written 12 months ago by pfs250
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 811 users visited in the last hour