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**# the Indel needs to have BF_LRE_LUD (a Bayes factor comparing a. related & HWE to b. unrelated & HWD) > -10. Higher BF_LRE_LUD should indicate a better Indel. We used Hyun's MiLK program to obtain BF_LRE_LUD values. Results for Indels on all chromosomes can be found here:
**# the Indel needs to have BF_LRE_LUD (a Bayes factor comparing a. related & HWE to b. unrelated & HWD) > -10. Higher BF_LRE_LUD should indicate a better Indel. We used Hyun's MiLK program to obtain BF_LRE_LUD values. Results for Indels on all chromosomes can be found here:
**#* /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/MiLK_filtering/all.genotypes.milk.sites.vcf
**#* /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/MiLK_filtering/all.genotypes.milk.sites.vcf
*** Overall results from all of the below filtering can be found here: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/FINAL/FinalIndelFilteringStatistics.txt
*** Overall results from all of the below filtering can be found here:
*** VCFs of Indels after filtering can be found here: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/FINAL/all.genotypes.*.PASS.vcf.gz
**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/FINAL/FinalIndelFilteringStatistics.txt
*** VCFs of Indels after filtering can be found here:
**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/FINAL/all.genotypes.*.PASS.vcf.gz
**** all.genotypes.PASS.vcf.gz
