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.  

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

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

*** (2) 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:

### (2) 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:

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/AnnotateIndels/All.annotated.sites.vcf.gz

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/AnnotateIndels/All.annotated.sites.vcf.gz

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/AnnotateIndels/Overlaps.txt

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/AnnotateIndels/Overlaps.txt

*** (3) at least 50% of the Indels should have informative AD field (we define "informative" to mean that the sample has U/(R+A+U)<0.50). Results for Indels on all chromosomes can be found here:

### (3) at least 50% of the Indels should have informative AD field (we define "informative" to mean that the sample has U/(R+A+U)<0.50). Results for Indels on all chromosomes can be found here:

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/filter2_output.txt

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/filter2_output.txt

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/INDEL_filtering_final.txt

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/INDEL_filtering_final.txt

*** (4) at least 50% of the Indels should have informative PL field (we define "informative" to mean that the PL field for the sample is anything BUT ././. or 0/0/0). Results for Indels on all chromosomes can be found here:

### (4) at least 50% of the Indels should have informative PL field (we define "informative" to mean that the PL field for the sample is anything BUT ././. or 0/0/0). Results for Indels on all chromosomes can be found here:

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/filter1_output.txt

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/filter1_output.txt

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/INDEL_filtering_final.txt

**** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/INDEL_filtering_final.txt

*** (5) 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:

### (5) 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