From Genome Analysis Wiki
Jump to navigationJump to search
No change in size
, 10:59, 27 June 2016
Line 44: |
Line 44: |
| *** 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 |
| | | |