coverage and SNP detection

rudi283 · 03-29-2011, 08:22 AM

Hi,

I was wondering if there is a standard rule about coverage and SNP detection. How many reads (paired end) do I need to be able to say that's a SNP. I heard that need to be above 30 but I'm a bit confused. Does that mean that if I've got for example 15 I can't say it's a SNP?
I was wondering as wel if I can say it's a SNP when for example all forward reads have the change but non of the reverse reads (reads in pairs)- what does it mean?
The same if for example coverage is 60 but the reads are only from the same direction-reads from the other direction don't reach that point. Can I say it's a SNP?

Please help
Thanks!

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Coverage "standards" for SNP detection in tumor samples	giorgifm	Bioinformatics	7	06-26-2013 03:41 PM
Coverage required for Sanger based SNP detection and Genotyping	gavin.oliver	De novo discovery	3	08-30-2011 01:41 AM
Coverage required for SNP detection?	Kasycas	De novo discovery	3	04-12-2011 11:38 PM
SNP Detection	Oxygen81	Bioinformatics	12	10-08-2010 12:50 PM
SNP detection	doxologist	Genomic Resequencing	14	09-06-2010 07:49 AM

03-29-2011, 08:22 AM	#1
rudi283 Member Location: europe Join Date: Sep 2010 Posts: 27	coverage and SNP detection Hi, I was wondering if there is a standard rule about coverage and SNP detection. How many reads (paired end) do I need to be able to say that's a SNP. I heard that need to be above 30 but I'm a bit confused. Does that mean that if I've got for example 15 I can't say it's a SNP? I was wondering as wel if I can say it's a SNP when for example all forward reads have the change but non of the reverse reads (reads in pairs)- what does it mean? The same if for example coverage is 60 but the reads are only from the same direction-reads from the other direction don't reach that point. Can I say it's a SNP? Please help Thanks!