Question: 1000 Variant Calling Parameters
0
gravatar for User 1933
6.9 years ago by
User 1933340
User 1933340 wrote:

I am sure not if I should ask this question here ! but I hope to get an answer. Before asking my question I read here http://www.1000genomes.org/analysis but couldn't find my answer. I wonder, with what setting the variant calling has been done in the 1000 genomes project. by setting, I mean, the minimum Read Depth, Confident, Call Quality;

1000genomes gatk • 1.5k views
ADD COMMENTlink modified 6.9 years ago by zam.iqbal.genome1.7k • written 6.9 years ago by User 1933340
1
gravatar for zam.iqbal.genome
6.9 years ago by
United Kingdom
zam.iqbal.genome1.7k wrote:

The 1000g did not use one pipeline with one set of parameters. They used (use) multiple pipelines run in different places, and then combined the results. Check out the supplementary material of the first two main papers.

ADD COMMENTlink written 6.9 years ago by zam.iqbal.genome1.7k

thanks - so how one can use 1000g to compare the significance of finding some variation in another cohort ?! Only based on the frequency of the variance ?!

ADD REPLYlink written 6.9 years ago by User 1933340

If you find some variation in another cohort, you can look to see if that site exists in the 1000g callset, and at what frequency it exists in the relevant populations, and on what haplotypic background, and compare with your cohort. I'm not sure what you want - is the idea that you want to be able to run the 1000g pipeline yourself, so you have truly comparable results with your new cohort?

ADD REPLYlink written 6.8 years ago by zam.iqbal.genome1.7k

My goal is to show the level of strength of our variants. I am told, reporting the frequency of the variant in 1Kg is not enough. I am thinking about a new strategy, such as runing the 1KG pipeline by myself and doing a 1-1 comparison. I appreciate any suggestion.

ADD REPLYlink written 6.8 years ago by User 1933340
1

I think you need to formulate your question better for us to be able to help. Do you have another cohort which is also a phenotype-free population? Or are you looking at a cohort of people with a disease, and you want to see the significance of new variants/of the variants that you find? I assume it is the second option, in which case you are basically doing a case-control study, on which there is a lot of literature (which I am not an expert in, sorry)

ADD REPLYlink written 6.8 years ago by zam.iqbal.genome1.7k

I am looking at the significance of new variants/of the variants. Thank you any way

ADD REPLYlink written 6.8 years ago by User 1933340
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