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Old 03-24-2012, 07:34 PM   #1
himanshu04
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Location: New York

Join Date: Mar 2012
Posts: 35
Default SNP detection using RSamtools

Hello everyone,
I have the pileup file built using Rsamtools, but when I call the snps using readPileup() , there is a error .
The command and error are :
Z = readPileup("ex1.pileup", variant="SNP")


Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings,
> :
> scan() expected 'an integer', got '^~.
I am stuck at this since morning. What should I be doing and Is there any other way to call snps in R.
Any help will be much appreciated.
Thanks,
Himanshu Sharma.
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Old 03-25-2012, 04:13 PM   #2
himanshu04
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Join Date: Mar 2012
Posts: 35
Default

Can any one help me with this please?. I am unable to figure it out. Thanks
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