Entering edit mode
9.6 years ago
deepue
▴
160
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
Thank you Irsan.
Could you also help me with my second question?
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, ...
Hi,
I have Human exome sequencing data with me. I would like to know how to know
If you stumble on this page and wonder, if there's a link, which is still up to date: Check this GATK-website link