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hackseq / 2016_project_6

Inferring sex chromosome and autosomal ploidy in NGS data
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DGV #11

Closed whitneywhitford closed 7 years ago

whitneywhitford commented 7 years ago

All DGV CNVs

X = 9170 CNVs Y = 1288 CNVs 19 = 12,175 CNVs

co-ordinates for GRCh38 from 2016-05-15 release http://dgv.tcag.ca/dgv/app/downloads?ref=

CNVRs (overlapping CNV regions, both del and dup) using bedtools (v 2.25.0) mergeBed X = 1422 CNVs, 107273677 bp (0.687 of chromosome) Y = 94 CNVs, 19087394 bp (0.334 of chromosome) 19 = 392 CNVs, 50635920 bp (0.863 of chromosome)

BED file can be found https://github.com/hackseq/2016_project_6/blob/master/Files/DGV_XY19all_mergedGRCh38.bed

whitneywhitford commented 7 years ago

DGV Gold standard CNVs

X = 1728 CNVs Y = 99 CNVs 19 = 3075 CNVs

co-ordinates for GRCh37 from 2016-05-15 release

CNVRs (overlapping CNV regions, both del and dup) X = 1285 CNVs, 3670595 bp (0.024 of chromosome) Y = 50 CNVs, 2981059 bp (0.052 of chromosome) 19 = 1593 CNVs, 50635920 bp (0.794 of chromosome)

BED file can be found https://github.com/hackseq/2016_project_6/blob/master/Files/DGV_XY19goldstd_mergedGRCh37.bed

whitneywhitford commented 7 years ago

NCBI remap used to convert DGV gold standard GRCh37 CNV coordinates to GRCh38

https://github.com/hackseq/2016_project_6/blob/master/Files/DGV/DGV_XY19goldstd_mergedGRCh38.bed