Question: SNP Calling Parameter Settings
1
gravatar for mcclintock
8 weeks 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 • 182 views
ADD COMMENTlink modified 23 days ago by Biostar ♦♦ 20 • written 8 weeks 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 8 weeks ago • written 8 weeks ago by Fabio Marroni2.1k

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

ADD REPLYlink written 8 weeks ago by mcclintock10
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