Hi all,
I want to use GATK for re-calibrating Q values, identify and calibrate variants (including indels) and create a VCF file for further analysis. I presently have a mapped BAM file from BWA. As I'm new to GATK I request someone to give me the commands to be used in GATK to get the VCF file. I had used the HG38 reference from NCBI for BWA.
Thanks for the help.
If you are interested in variant discovery as it seems, and assuming you have GATK version 3.3, you have to use HaplotypeCaller as the UnifiedGenotyper has been deprecated. I will recommend going through GATk's tools documentation here:
https://www.broadinstitute.org/gatk/guide/tooldocs/#VariantDiscoveryTools.
Use GATK best practices https://www.broadinstitute.org/gatk/guide/best-practices. They have given very nice explanation step by step. Follow them. You will get your answer.
Hi this might not answer your GATK question but you might find it interesting. Google Brain Team recently released DeepVariant which you can use as an alternative to GATK.
We implemented a reproducible version that was submitted to NF-Core (https://lifebit.page.link/UW58).
We also made it available in Lifebit (https://lifebit.page.link/os1m) if you want to try it with example parameters.
In practice, DeepVariant first builds images based on the BAM file, then it uses a DeepLearning image recognition approach to obtain the variants and eventually it converts the output of the prediction in the standard VCF format.
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