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het/hom ratio of exome samples
We have sequenced whole exomes of a family with monogenic disease. The sequencing was done on Solid 5500 as single-end and data processed by Lifescope. We have got different QC metrics for the produced VCF files. Based on the metrics one sample is standing out because it has a het/hom ratio of 3, and all others have values between 1.4 and 1.6. Of course this sample also has the largest reads output (larger xsq files and bam files) and therefore has the highest number of SNPs (60000 vs. ~50000 from others). Other metrics e.g. Ti/Tv ratio and %dbSNP are fine.
Googling for "het/hom ratio" I found that in a few published papers this ratio is mostly in a narrow range, 1.4 to 1.6. This makes us worrying if there is something really wrong with this sample. We have asked the people who did the experiment could there be a sample mixup but they cannot tell much. So I would like to hear what are your experiences with het/hom ratio in whole exome samples. Also pointer to references is highly appreciated because I found there are very few papers mentioned this.
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