87
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Locations of Files for Current Data Freeze of 3839 Samples
NOTICE: We identified late in the process that two of the samples (22855 and 22385) were actually the same individual. They both should be the same individual 22855. Therefore, there are 3840 sample IDs in each of the files below, but only 22855 should move on to later processes. In future data freezes with this data, these two sequencing sets should be merged into a single 22855 individual.
NOTICE: We identified late in the process that two of the samples (22855 and 22385) were actually the same individual. They both should be the same individual 22855. Therefore, there are 3840 sample IDs in each of the files below, but only 22855 should move on to later processes. In future data freezes with this data, these two sequencing sets should be merged into a single 22855 individual.
* List of Sample Numbers
* List of '''Sample Numbers'''
**
**
* List of paths to BAMs used in this data freeze (Index file)
* List of paths to '''BAMs''' used in this data freeze (Index file)
** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/SNPCALL/FINAL_index_20150504.index
** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/SNPCALL/FINAL_index_20150504.index
* Pedigree (Not too helpful -- used for SNPCall)
* '''Pedigree''' (Not too helpful -- used for SNPCall)
** All Samples: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/SNPCALL/FINAL_ped_20150510.ped
** All Samples: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/SNPCALL/FINAL_ped_20150510.ped
* QC Summary
* '''QC''' Summary
**
**
* SNPCall Results (Produced with Gotcloud SNPCall and phased using Beagle4)
* '''SNPCall''' Results (Produced with Gotcloud SNPCall and phased using Beagle4)
** /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
