acceptable coverage

Question

acceptable coverage

przemekl opened this issue 6 years ago · comments

Przemek commented 6 years ago

What is an acceptable sequencing depth level?
I have almost 75% of the variants identified as "S: No read cover".

Ruibang Luo · Answer 1 · Tue May 29 2018 21:28:47 GMT+0800 (China Standard Time)

I've not tested depth below 30x. What's the average depth of your sample?

Przemek · Answer 2 · Wed May 30 2018 23:17:46 GMT+0800 (China Standard Time)

30x (counted by 'samtools mpileup') or 27x (counted by samtools mpileup -aa)

Ruibang Luo · Answer 3 · Fri Jun 01 2018 16:28:21 GMT+0800 (China Standard Time)

I've tried 3 different depths (10x, 25x and 50x) on the GIAB HG001 sample with ~3.6M known variants. The "S: No read cover" remain low for all three (627, 315 and 273). The number of "X: Mismatch" at 25x is 1.5x higher than the 50x. In contrast, 10x is ~10x higher than the 50x. In your case, 75% of the variants identified as "S" is likely to be a result of inappropriate inputs. I've updated the code to include some validity checks on the inputs, please try again and let me know that doesn't help. Thanks.

Przemek · Answer 4 · Tue Jun 05 2018 20:05:09 GMT+0800 (China Standard Time)

After your recent fixes, number of variants identified as "S: No read cover" has dropped to 12,5%. Such a number is acceptable. Please, close this issue.