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Old 08-10-2011, 12:30 AM   #1
ozs2006
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Location: rishon le zion ,israel

Join Date: May 2010
Posts: 21
Smile 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
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