Minimum coverage for structural variant calling
1
0
Entering edit mode
3.5 years ago
5utr ▴ 370

Does anybody have experience/references for trying to identify SVs with very low coverage (~1x) WGS data? Is it even worth doing it or are the results completely untrustworthy?

variant structural coverage • 844 views
ADD COMMENT
1
Entering edit mode
3.5 years ago
Zhilong Jia ★ 2.2k

“Overall, low-coverage WGS strategies detect drastically more gold standard CNVs compared with arrays and are accompanied with smaller percentages of CNV calls without validation. Furthermore, we show that WGS (at ≥1× coverage) is able to detect all seven gold standard deletion CNVs >100 kb in NA12878, whereas only one is detected by most arrays. Lastly, we show that the much larger 15 Mbp Cri du chat deletion can be readily detected with short-insert paired-end WGS at even just 1× coverage.”

ref: https://jmg.bmj.com/content/55/11/735.long

ADD COMMENT

Login before adding your answer.

Traffic: 1918 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6