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Old 12-23-2013, 01:28 AM   #1
rnahar
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Default VarScan Indels output to Annovar input

Hi
I am using Varscan for calling somatic SNPs and Indels and Annovar for annotation. However for indels the way it represents reference allele is 1 base upstream of the actual insertion/deletion. Is there a way to convert it to the annovar input format ?
thanks
Rahul
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Old 12-23-2013, 03:35 PM   #2
m_two
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Is your problem the same as the one described here: http://seqanswers.com/forums/showthread.php?t=20000

IsmailM posted a solution on 07-25-2013, 05:17 PM #19
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Old 12-23-2013, 08:31 PM   #3
rnahar
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My problem is the +/- in denoting indels as also discussed on the other thread - However I do not use the vcf output but standard tabular output so cannot use Ismail's solution. Will also post on the other thread.
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