What's 1000 Genome indel calls??

Question

[2012secondseason]

Hi. Studing tool of RealginerTargetCreator, I'm faced with a curious problem.

--known / -known Input VCF file with known indels Any number of VCF files representing known SNPs and/or indels. Could be e.g. dbSNP and/or official 1000 Genomes indel calls. SNPs in these files will be ignored unless the --mismatchFraction argument is used.

About this argument, what's 1000 Genomes indel calls? It is made of someone's genome? I don't understand that why I need information of one person's indel record at using this tool.

Thanks.

Answer 1

[h.mon]

The 1000 Genomes InDel calls is made on two trios, not one individual. And Broad provides sets of known indels with 1000 Genomes + Mills - probably from An initial map of insertion and deletion (INDEL) variation in the human genome, and I have no idea how many individuals were genotyped there.

The importance of the known sites is explained at the Broad online documentation: What should I use as known variants/sites for running tool X?

[2012secondseason]

Nice explanation. Thank you very much!

[enigmargs]

h.mon Hi, 1000Genomes+Mills hyperlink leads to an article where the link to resource is broken. But the updated GATK resource bundle only has hg38 files. I have bam files mapped to hg37 reference (not sure whether it's from GATK bundle). It would be great if you could please direct me to the site where I can download all the resources shown in GATK bundle but for hg37?