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Old 01-14-2013, 02:53 AM   #1
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Question Weird annovar output after variant calling

Hello all,

I ran Annovar recently and I'm currently analyzing the results.
I gained an output file (tab delimited file) with 11 colums.
An example entry is given here:
avsift 0.53 chr1 10335315 10335315 G A hom 28.1 6 20

I followed the steps on this website:
where i went to link 2 "Samtools genotype-calling pileup format"
and then looked at the 3rd code block.

The example stated on their website is pretty straight forward and easy to understand. The problem however is that in my case i have 11 instead of 9 columns, and the last column (used for the number of mutations found in the total amount of reads for that position) is 99% of the time '20'.

This is also the case for a read depth lower then 20.
(So there are cases of a nucleotide found 4 times total, with 20 of those being labeled as SNP...)

My question is: Did other people run into this or do people know how to fix this?

My current sollution would be a workaround to make a script which searches for the SNP in the annovar output format and then generate the last column by searching for the given position in the mPilup file.
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Old 01-17-2013, 04:30 AM   #2
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Pease, anyone?
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annovar, column, mpileup, variant calling

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