I am following the GATK best practices workflow on Linux. I am using chr21.fa as reference from NCBI and .vcf files are taken from resource bundle and dbsnp.vcf is from NCBI. I am working on the VariantRecalibrator step. It gives me NullPointerException. I am attaching the console error that I have got which contains the command also and raw_variants.vcf which is generated in previous step by HaplotypeCaller tool in txt format. Please let me know what can be the issue.
I am using GATK 2.7.2. I am working on the Best practices of GATK. I have followed all the steps as mentioned for Best practices. All the .vcf files that are needed as input are downloaded from ftp bundle/2.3/h37.
In Variant Recalibration step: I am using HaplotypeCaller tool to generate the raw_variants.vcf The .vcf is generated but it consist of only headers and no variants for the same. Due to this issue the VarianRecalibration tool is not working as it needs annotation.
I am attaching the raw_variants.vcf that is generated after executing HaplotypeCaller tool.
I have one more question: Whether the HaplotypeCaller adds quality score in the output .vcf file?
I am using GATK 2.7.2. I am working on the Best practices of GATK. I have followed all the steps as mentioned for Best practices. I want to Generate before/after plots. This is done by the following command
-T AnalyzeCovariates -R ReferenceFiles\sequence.fasta -l DEBUG -before ReferenceFiles\recal_data.table -after ReferenceFiles\post_recal_data.table -plots ReferenceFiles\recalibration_plots.pdf
On running this command I get the error. Please refer attachment for error : “GATK_AnalyzeCovariant_Error.txt”
After referring the forums on the http://www.broadinstitute.org : -I have already installed R script and set R_HOME in my environment variables and also in the path. -I have copied the BQSR.R in the GATK tools folder. -I have installed the gsalib package in R -I have installed the ggplot2 package in R -Since I thought It can be network proxy issue, I have also registered on http://www.broadinstitute.org forum and asked for the .key file which is used to disable "phone-home" feature that sends us information about each GATK run via the Broad file system (within the Broad) and Amazon's S3 cloud storage service (outside the Broad). It will be reviewed by them and then I can get my key.
Please help me to know what exactly can be the issue.