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, 11:29, 27 June 2016
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| *** 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. |
− | *** Overall results from all of the below filtering can be found here: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/FINAL/FinalIndelFilteringStatistics.txt
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− | *** VCFs of Indels after filtering can be found here: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/FINAL/all.genotypes.*.PASS.vcf.gz
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| **# 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: |
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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 |
| + | *** VCFs of Indels after filtering can be found here: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/FINAL/all.genotypes.*.PASS.vcf.gz |
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