Question: How many SNPs I should expect to see in a normal human embryonic stem cell (hESC) with WES analysis?
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gravatar for maria2019
12 months ago by
maria201990
maria201990 wrote:

I have a normal human embryonic stem cell line (hESC) and the WES data analysis gives me 109313 SNP and 9943 Indel results. Are these numbers normal for a NORMAL cell line? I was thinking since this is a normal cell line it should not have many SNPs. For the SNP calling I used samtools and I did not do any special filtering ( like count of the reads covering the position of the SNP). Should I do some sort of special filtering?

hesc snp samtools wes • 285 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by maria201990

Yes. That is roughly normal. You expect to see millions of SNPs across the entire individual genome. The exome covers only about 2% of that, but that still leaves you with plenty.

You might find these previous discussion helpful:

ADD REPLYlink modified 12 months ago • written 12 months ago by igor9.8k
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