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Hi, For both IndelRealigner/RealignerTargetCreator, there is an option for known indel sites as below:
However, from the bundle files collection such as from hg19, there are several vcf files:
1000G_indels_for_realignment.hg19.vcf 1000G_omni2.5.hg19.sites.vcf 1000G_omni2.5.hg19.vcf dbsnp_132.hg19.excluding_sites_after_129.vcf dbsnp_132.hg19.vcf hapmap_3.3.hg19.sites.vcf hapmap_3.3.hg19.vcf indels_mills_devine.hg19.sites.vcf indels_mills_devine.hg19.vcf NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.sites.vcf NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf
amongst them, just based on the names, 1000G_indels_for_realignment.hg19.vcf and indels_mills_devine.hg19.sites.vcf look like the files supposed to use for IndelRealigner/RealignerTargetCreator, Could you clarify the exact files for this purpose?
Since for old version, I have used 1000G_phase1.indels.hg19.vcf and Mills_and_1000G_gold_standard.indels.hg19.sites.vcf. and I compared the new and old files, quite different now.