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08-10-2011, 01:30 AM
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#1 |
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Member
Location: rishon le zion ,israel Join Date: May 2010
Posts: 21
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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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08-10-2011, 07:55 PM
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#2 |
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Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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Please do not submit the same post twice. Thank-you!
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08-10-2011, 11:04 PM
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#3 |
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Member
Location: rishon le zion ,israel Join Date: May 2010
Posts: 21
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I'm sorry,
Oz |
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| Tags |
| editing, igv, variants, varscan |
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