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Old 10-20-2010, 06:19 PM   #1
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Question Samtools SNP Caller versus MAQ SNP caller

I have been using MAQ's variant caller to call SNPs. I now want to use varfilter and want to make sure that I maintain the same conditions I had for MAQ. My question is which of the parameters are common to MAQ and Samtools' variant caller?

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Old 10-21-2010, 05:25 AM   #2
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Take a look to this .
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Old 05-18-2011, 07:42 AM   #3
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Default MAQ SNP caller

Dear all,

In need to know if MAQ SNP caller takes .bam files in input.

I have aligned reads by Novoalign and I want to use MAQ only as a SNP caller, is it possible or the alignment with MAQ is mandatory?

Waiting for your feedback,
Thanks a lot

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Old 05-18-2011, 09:00 AM   #4
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No, MAQ does not take BAM files as input. Use "samtools pileup -A", however "pileup" will be removed from samtools in the next release, so you might as well move over to "samtools mpileup".
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Old 05-18-2011, 11:19 PM   #5
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Thanks a lot,
I used samtools pileup and I had no problem, but I would like to try with an other SNP caller, for example MAQ.
So, as far as I understood, It is not possible to call variants with MAQ starting with reads aligned by Novoalign. If I want to call variants with MAQ I had to re-align my reads with MAQ. Is it correct?

Thank you in advance for your suggestions.

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Old 05-18-2012, 01:41 PM   #6
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This may be a dead thread, but just in case, I believe the old version of samtools pileup (the new version is samtools mpileup) can be forced to produce the MAQ consensus call (it requires a special option, -c). Also, if you are interested in another caller, the pileup can be used as input to the BSNP genotype caller at .
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