Question: NGS to find SNPs
0
gravatar for DanielC
22 months ago by
DanielC100
Canada
DanielC100 wrote:

Dear All,

I am working on NGS analysis, I do not have much experience in this. I would really appreciate response from experienced personnels to share the steps of how to do NGS analysis to find SNPs effectively, where one is provided with fastq files of the reads.

Thanks much, DK

snp • 577 views
ADD COMMENTlink modified 22 months ago by Kevin Blighe51k • written 22 months ago by DanielC100
3
gravatar for genomax
22 months ago by
genomax74k
United States
genomax74k wrote:

GATK Best practices linked below glosses over alignments, which are obviously required to follow the steps in the guide. You can use any of the many NGS aligners available (BBMap, BWA, Bowtie2, if you are doing genome alignments) (BBMap, STAR, HISAT2 if you need a splice-aware aligner). Pick an aligner and then stick with it, once you understand its options (there are many for most and they are all program specific). You would also need access to a reference genome and will have to create search indexes (that are again aligner specific).

ADD COMMENTlink modified 22 months ago • written 22 months ago by genomax74k
2
gravatar for WouterDeCoster
22 months ago by
Belgium
WouterDeCoster42k wrote:

Have a look at the GATK best practices.

ADD COMMENTlink written 22 months ago by WouterDeCoster42k
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