Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
error with GenotypeGVCFs
java -Xmx10g -jar $gatk -T HaplotypeCaller \ -R $refGenome \ --dbsnp $dbSNP \ -o s1.raw.var.g.vcf.gz \ -I s1.bam \ -pairHMM VECTOR_LOGLESS_CACHING \ --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 && java -Xmx10g -jar $gatk -T GenotypeGVCFs \ -R $refGenome \ --variant s1.raw.var.g.vcf.gz \ -o s1.raw.var.vcf.gz
Error in GenotypeGVCFs :
ERROR MESSAGE: Line 115: there aren't enough columns for line ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½uNï¿½ï¿½ï¿½ï¿½Þ«rfï¿½ebhï¿½ï¿½ï¿½ï¿½ï¿½NH(ï¿½ï¿½ï¿½ï¿½Ù»atï¿½ ï¿½Eï¿½;J1ï¿½ï¿½ï¿½ï¿½Xï¿½ï¿½Ê©áï¿½ï¿½ï¿½Çï¿½ï¿½ï¿½ï¿½ï¿½>ï¿½ï¿½@ï¿½ï¿½,0ï¿½ï¿½' (we
expected 9 tokens, and saw 2 ), for input source: s1.raw.var.g.vcf.gz