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07-14-2011, 09:07 AM
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#1 |
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Member
Location: Edinburgh Join Date: Mar 2010
Posts: 16
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consensus from mpileup
Hi,
I am trying to call the consensus sequence from an mpileup file using samtools (specifically the vcf2fq command). The consensus fastq file is produced, and looks correct, but during the running of vcf2fast I receive the following error(?) numerous times: Argument "MRSA252^I2001121^I.^IA^I.^I28.2^I.^IDP=1;;CI95=1.5,0;FQ=..." isn't numeric in numeric lt (<) at /samtools-0.1.16/bcftools/vcfutils.pl line 503, <> line 1958656. Could anyone explain to me what this means, and whether I am doing something wrong?! Cheers Paul |
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07-14-2011, 09:08 AM
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#2 |
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Senior Member
Location: San Diego Join Date: May 2008
Posts: 912
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I don't think anything is wrong. It does that at every point where the DP is 1 or 0. The software will fill in N's at those points. Just let it finish, the look at it, it should be alright.
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07-14-2011, 09:10 AM
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#3 |
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Member
Location: Edinburgh Join Date: Mar 2010
Posts: 16
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Thank you!
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07-14-2011, 09:11 AM
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#4 |
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Member
Location: Edinburgh Join Date: Mar 2010
Posts: 16
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Thank you!!
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