Entering edit mode
4.9 years ago
yoh1242
▴
10
Hello! I need a step to step Guide on how to Create a Truth and Training set for VariantRecalibrator GATK v4.1.4. The Guide available on GATK website was not helpful enough and I have yet to make progress.
I have downloaded a list of known indels BQSR file from 1000bullgenome website and plan to use it for the -resource part of the command line. Kindly mention the steps necessary to turn this file into a suitable resource file for variant recalibrator step of GATK.
Where did you face problems? Which guide are you referring to and how far did you get?
I have performed HaplotypeCaller but can not proceed with VariantRecalibrator due to lack of resource file.
I have downloaded 1000bullgenome.vcf and performed VariantCalling and VariantFIltration on the file but when I run the Commandline.
I get the following Error:
I have tried both GATK Variant Annotator and snpEff on the resource vcf file but nothing is working.
You've still not pointed us to the "guide available on GATK website" you refer to.
I cant seem to find the link on the new GATK forum. Regardless, The steps were as follows: Perform SelectVariants, followed by VariantFiltration and finish it with Variant Annotation on the known SNP and Indel vcf file to create a Training Set resource file. Despite following this step I have yet to yield any result
Hello yoh1242!
Is this a follow-up question for above thread or are you basically asking the same question again?
DIfferent but same question.
I am asking for sites where I can download -resource vcf files for this very question mentioned here