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, 10:57, 27 June 2016
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| * 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: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/snpEff/* |
| + | *** VEP: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/VEP/* |
| + | ** We used an Indel filtering strategy composed of many levels. |
| + | *** (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: |
| + | **** /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 |
| + | *** (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/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: |
| + | **** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/filter1_output.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: |
| + | **** /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/MiLK_filtering/all.genotypes.milk.sites.vcf |
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| * mtDNA Copy Number Summary | | * mtDNA Copy Number Summary |
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| ** Overall discrepancy can be found: | | ** Overall discrepancy can be found: |
| *** IN PROCESS | | *** IN PROCESS |
| + | |
| + | * Sample Name Conversion |
| + | ** The CSCT samples had two different names.... a numeric and an alphanumeric. The conversion key can be found here: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/SampleNameChanges.txt |
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| === What is Complete === | | === What is Complete === |