Changes

*** VEP: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/VEP/*

*** VEP: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/VEP/*

** We used an Indel filtering strategy composed of many levels.  

** We used an Indel filtering strategy composed of many levels.  

**# AC must be 1 or greater -- eliminate Indels with AC=0

**# AC must be 1 or greater -- eliminate Indels with AC=0

**# the Indel should overlap with a VNTR region or overlap with another Indel. We used Adrian's annotate indels program to identify such overlaps. Results for Indels on all chromosomes can be found here:

**# the Indel should overlap with a VNTR region or overlap with another Indel. We used Adrian's annotate indels program to identify such overlaps. 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:

**# 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