Dear all
I have generated Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
with tabix
when running RealignerTargetCreator should indicate the tbi file among the inputs?
is it correct to us use -known Mills_and_1000G_gold_standard.indels.hg38.vcf or should I use
-known Mills_and_1000G_gold_standard.indels.hg38.vcf,gz
java-new -jar ../GenomeAnalysisTK.jar -T RealignerTargetCreator -R Homo_sapiens_assembly38.fasta -I unodedupsorted474_1_riccio-161221_GAATCTGA.bam -known Mills_and_1000G_gold_standard.indels.hg38.vcf -o unotarget_intervals.list &
thank you
vittoria