Entering edit mode
6.4 years ago
Ramana
•
0
Hi, I tried to generated a .VCF file using GATK HaplotypeCaller. I provided all the input requirements hg38.fa, hg38.dict, hg38.fa.fi and Bam file. Java 1.8 and picard
I'm getting this error, kindly reply.
Command : java -jar GenomeAnalysisTK.jar HaplotypeCaller -R /home/Downloads/GenomeAnalysisTK-3.8-0-ge9d806836/hg38.fa -I /media/CANCERGENOMICS/NA12878.bam -o /home/Downloads/GenomeAnalysisTK-3.8-0-ge9d806836/NA12878GATK.vcf
INFO 12:15:43,860 HelpFormatter - ---------------------------------------------------------------------------------- INFO 12:15:43,862 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
