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-   -   Visualization of variants from varScan with IGV (http://seqanswers.com/forums/showthread.php?t=13349)

ozs2006 08-10-2011 12:30 AM

Visualization of variants from varScan with IGV
 
Hi all,

I visualized the variant positions I got from varScan using IGV.
I saw that they show different coverage from what I have detected using varScan (usually the IGV have higher coverage for both variant and reference).
This was also the case when I only used filtering for variant base quality>=15 and the other filtering steps done by awk on the output files.

Example:
from varScan output:
chr1 556810 T Y 4625 254 5.21% 2 2 30 30 0.98 1 1 2266 2359 3 251 C

from IGV:

chr1 556810:
A: 169 (2%,0+,169-)
C: 692 (8%, 5+, 687-)
T: 7551 (90%, 4316+, 3225-)
N: 0

Does anyone know where I got wrong?

Thanks in advance,
Oz

nilshomer 08-10-2011 06:55 PM

Please do not submit the same post twice. Thank-you!

ozs2006 08-10-2011 10:04 PM

I'm sorry,
Oz


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