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** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/SNPCALL/beagle4/chr*/chr*.filtered.PASS.beagled.vcf.gz
** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/SNPCALL/beagle4/chr*/chr*.filtered.PASS.beagled.vcf.gz
* IndelCall Results (Produced with Gotcloud Indel)
* '''IndelCall''' Results (Produced with Gotcloud Indel)
** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/indel/final/all.genotypes.sites.vcf.gz
** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/indel/final/all.genotypes.sites.vcf.gz
** SNPEff and VEP declarations of Indel types can be found:
** SNPEff and VEP declarations of Indel types can be found:
*** SNPEff: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/snpEff/*
*** SNPEff: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/snpEff/*
*** 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:
