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Old 12-18-2011, 11:23 PM   #1
meher
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Default samtools mpileup error

Hi all,

i am trying to call snp's using mpileup command in samtools and i got the following error, could anyone give your suggestions to fix this!!


incorrect number of fields (4 != 5) at 4:53820987
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Old 12-19-2011, 08:55 AM   #2
swbarnes2
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The usual answer is that your .bam file is truncated.
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Old 12-19-2011, 08:58 AM   #3
meher
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so should i regenerate the file. But, with this file i have generated output using mpileup when i did for the first time, for some reason it showed this error when using it for the second time.
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Old 10-09-2012, 12:47 AM   #4
figo1019
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Quote:
Originally Posted by meher View Post
Hi all,

i am trying to call snp's using mpileup command in samtools and i got the following error, could anyone give your suggestions to fix this!!


incorrect number of fields (4 != 5) at 4:53820987
Hello Meher

I am also getting a similar problem using the mpile up, have you sorted out this problem?

Regards
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