Question: calling 1000G SNPs/indels from ngs data (chipseq or other source)
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gravatar for Tafelplankje
4.3 years ago by
Tafelplankje120
Netherlands
Tafelplankje120 wrote:

I would like to call known (e.g. from 1000G project) SNPs and indels from sequence reads, in my case a chip-seq project with 20 samples. Is there an easy way to call known SNPs/Indels ? (How) should i take into account the Indels/SNPs during allignment (because an indel is could be quite different from the reference genome)?

ADD COMMENTlink modified 4.1 years ago • written 4.3 years ago by Tafelplankje120
0
gravatar for RamRS
4.3 years ago by
RamRS20k
Houston, TX
RamRS20k wrote:

AFAIK you can incorporate such info in the variant calling step with GATK's Variant Recalibration 'known variants' option. Not sure if you can take variants into effect at during assembly.

EDIT: I meant to tell you of the "known variants" option available with GATK, not the Variant Recalibrator. I apologize for the confusion.

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by RamRS20k
0
gravatar for Ying W
4.3 years ago by
Ying W3.9k
South San Francisco, CA
Ying W3.9k wrote:

Maybe this is what you are looking for: http://www.bioconductor.org/packages/release/bioc/html/FunciSNP.html

ADD COMMENTlink written 4.3 years ago by Ying W3.9k
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