Question: Hom vs Het Variant calls
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gravatar for hellbio
4.4 years ago by
hellbio360
hellbio360 wrote:

Hi all,

I have a variant detected in four samples using samtools-0.1.19 as shown below

In one of the sample it is identified as "het" variant with 1 RefAllele reads and 7 AltAllele reads whereas it is identified as homozygous variant in the other three samples. We did preformed capillary sequencing in the lab and it turned out to be homozygous in all the samples.
Would you please let me understand the method behind the algorithm which led to identify the variant as heterozygous?


chr30    37342399    .    C    T    95.3    .    DP=5;VDB=4.238324e-02;AF1=1;AC1=2;DP4=0,0,3,2;MQ=60;FQ=-42    GT:PL:GQ    1/1:128,15,0:27

chr30    37342399    .    C    T    149    .    DP=9;VDB=3.473591e-02;AF1=1;AC1=2;DP4=0,0,2,7;MQ=60;FQ=-54    GT:PL:GQ    1/1:182,27,0:51

chr30    37342399    .    C    T    220    .    DP=14;VDB=1.072004e-01;AF1=1;AC1=2;DP4=0,0,6,8;MQ=60;FQ=-69    GT:PL:GQ    1/1:253,42,0:81

chr30    37342399    .    C    T    102    .    DP=8;VDB=1.068485e-01;RPB=8.141118e-01;AF1=0.5263;AC1=1;DP4=0,1,1,6;MQ=60;FQ=-17.1;PV4=1,0.035,1,0.42    GT:PL:GQ    0/1:132,0,10:13

samtools • 1.7k views
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