Variant caller reports a homozygous variant genotype, but more reads are associated with reference

Question

[rebeliscu]

Hi there,

I'm confused about how to interpret this output from calling variants using bcftools:

#CHROM      POS ID REF ALT    QUAL FILTER                                                                                                                     INFO   FORMAT       GSM5292852
1065632   chr9 41242177  .   T   C 6.65947      . DP=37;VDB=0.133454;SGB=-0.662043;RPBZ=2.91136;MQBZ=4.0715;BQBZ=1.05041;SCBZ=-0.480069;MQ0F=0;AC=2;AN=2;DP4=0,26,0,9;MQ=5 GT:PL:AD 1/1:34,24,0:26,9

In particular, I'm confused by the genotype being reported as 1/1 while the number of reads mapping to the reference vs. the alternative allele are 26 and 9, respectively.

Wouldn't this indicate a heterozygous or possibly homozygous ref. genotype?

Any insight would be much appreciated.

Answer 1

[colindaven]

You're right, but MQ=5 - so this is a really poorly mappable region.

Check the QUAL field - here 6.6 - against more typical and robust SNPs you've found. I bet it is at the lower range of the QUAL distribution - but don't use bcftools for SNP calling myself.

[rebeliscu]

Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made.

Thanks for your answer!