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, 11:28, 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 |
| + | **** VCFs of Indels after filtering can be found here: /net/sardinia/progenia/SardiNIA/VariantCalling_20150330/INDELCALL/filterIndels/FINAL/all.genotypes.*.PASS.vcf.gz |
| **# 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: |