Question: What's 1000 Genome indel calls??
0
gravatar for 2012secondseason
12 months ago by
2012secondseason10 wrote:

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.

ADD COMMENTlink modified 12 months ago by h.mon24k • written 12 months ago by 2012secondseason10
2
gravatar for h.mon
12 months ago by
h.mon24k
Brazil
h.mon24k wrote:

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?

ADD COMMENTlink modified 12 months ago • written 12 months ago by h.mon24k

Nice explanation. Thank you very much!

ADD REPLYlink written 12 months ago by 2012secondseason10
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