GATK BaseRecalibrator Knownsites - where to download for vcf for human exome sequencing analysis ?

Question

[deepue]

Hi,

Where can I find the latest vcf files for human exome sequencing analysis in GATK, BaseRecalibrator -KnownSites?

I understood that this is not an optional parameter. How can we find unknown SNPs which were not reported in the file ?

Thanks

Answer 1

[Irsan]

Download the GATK resource bundle. See here for instructions.

[deepue]

Thank you Irsan.

Could you also help me with my second question?

[Irsan]

I don't understand your second question. "How can you find unknown SNPs not reported in some file?" Do you mean you have sequencing data yourself and you want to find SNPs (definition = >1% MAF in general population) not previously reported as SNP? Or do you want to find single nucleotide variants/insertions/deletions (SNVs and/or INDELs) in your data that are not reported as SNP? Or don't you have any data at all and you want to know what fraction of the genome has not been reported as polymorphic by any of the human variantion projects like 1000G, ESP, ...

[deepue]

Hi,

I have Human exome sequencing data with me. I would like to know how to know

1. SNPs which are not previously reported as SNP in the file which we are donwloading from GATK.
2. Will there be any difference on the SNP output, based on the type of file which we are giving as input to KnownSites ? (from GATK, another sources)

[Oliver]

If you stumble on this page and wonder, if there's a link, which is still up to date: Check this GATK-website link