How to get the genetic heterogeneity based on NGS?

[hugomarquez]

How should I get the information of genetic heterogeneity based on NGS?

That is to say, how many times each SNP appears in one site in all reads?

For example, for one SNP at chr1:1000000, it appears in two reads out of 100 reads. For another SNP at chr2:2000000, it appears in 50 reads out of 60 reads.

Does anyone know how I can get such information? Is bcftools applicable for this use? Thanks so much.

[dpryan]

The term to google for is "SNP calling", which would have turned up samtool mpileup followed by bcftools and GATK, which are probably the two most popular programs (though far from the only ones).

[blancha]

https://www.broadinstitute.org/gatk/...t-analysis-ovw