Question: SNP Calling Parameter Settings
1
gravatar for mcclintock
10 months ago by
mcclintock10
China/Wuhan/HUST
mcclintock10 wrote:

Hi everyone,

I am using family trios data to run GATK's SNP calling pipeline. The HaplotypeCaller gave me the father's SNPs file, which I have recalibrated using VariantRecalibrator. But the final VCF file still has 3 million “PASS” records. Actually, one human has no chance to carry so many SNPs.

Any advice for adjusting the parameters?

The parameters I used refer to the literature below.

Roazen, D., Thibault, J., Banks, E., Garimella, K., Altshuler, D., Gabriel, S. and DePristo, M. (2013). From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Current Protocols in Bioinformatics, pp.11.10.1-11.10.33.

Thanks.

snp gatk vcf • 344 views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 10 months ago by mcclintock10

Actually, one human has no chance to carry so many SNPs.

Why do you think so? What is the expected number of SNPs for one human subject on average?

ADD REPLYlink modified 10 months ago • written 10 months ago by Fabio Marroni2.4k

A little more than 2 million is appropriate, as far as I know.

ADD REPLYlink written 10 months ago by mcclintock10
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