I am still new in bioinformatics field and now I am having an internship in MGI. Recently, we are given 2 sets of exome data which are diabetes type1 and diabetes type2. We already did with pre-processing and reference genome assemble, now we have to proceed to variant calling in order to find SNP variant in the exome., but we are not sure which of the variant caller is suitable for us to use. GATK or Varscan? Anyone can provide the pipeline for us?
There are several tools you can use. Either you can analyze using a single tool or you can use a combination of different tools and choose data that are common. For example mutect2+Varscan2+Muse+Somatic Sniper. To start with you can follow this TCGA pipeline which involves GATK variant calling.
https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
We also use a python based pipeline if you have a huge dataset.
https://github.com/solida-core/diva
GATK is best, further you can mine/filter your variants using 1000 genomes/ clinvar/60KExome sets etc.,. lot of tools available for annotation including ensemble's variant effect predictor which almost include every other annotation like SIFT/POLYPHEN/GERP etc.,
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