Dear friends,
before using known variants like mills_vcf = "Mills_and_1000G_gold_standard.indels.hg38.vcf.";
kgenomes_phase1_vcf = "1000G_phase1.snps.high_confidence.hg38.vcf";
kgenomes_omni_vcf = "1000G_omni2.5.hg38.vcf";
dbsnp138_vcf = "Homo_sapiens_assembly38.dbsnp138.vcf";
hapmap_vcf = "hapmap_3.3.hg38.vcf";
do I need to run tabix? or the idx file is generated by gatk?
I noticed that when I run
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
a idx file was generated
if I need to run tabix, where do I find it?
thank you vittoria