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Old 06-20-2014, 01:52 AM   #1
StefanP
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Location: New Zealand

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Default samtools bcftools no FQ value

Hello,

I'm using the samtools/bcftools/vcfutils pipeline to call consensus sequences. However, I always get an warning:

Use of uninitialized value $q in numeric lt (<) at vcfutils.pl line 508, <> line 16742.
Use of uninitialized value $q in addition (+) at vcfutils.pl line 518, <> line 16742.

Which seams to be a problem with the FQ values. I checked the bcftools view -cg output and it doesn't record the FQ value. So, I think that's what's causing the problem.

Any idea why it doesn't provide the FQ value? And how to make it to? (I tried samtools 0.1.18 and 0.1.19).

Thanks,
Stefan
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Old 06-20-2014, 02:39 PM   #2
swbarnes2
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For starters, it would help if you posted your command lines, the versions of each piece of software, and a sample line from your .vcf

I'm wondering if you are using a very old version of samtools
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Old 06-20-2014, 02:51 PM   #3
StefanP
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Hi,

I use:

samtools mpileup -uf "$REFSEQ" ${bn}.sorted.bam | bcftools view -cg - | perl vcfutils.pl vcf2fq > ${bn}.fq

So the standard consensus call.

The output is here:

##fileformat=VCFv4.0
##samtoolsVersion=0.1.18 (r982:295)
##fileformat=VCFv4.0
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT processed_MS83_S20_L001.dup.sorted.bam
NC_002008 1 . G T 46 . DP=11;VDB=0.0000;AF1=0.500;AFE=0.500;DP4=3,0,8,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 76,0,85:0/1:78
NC_002008 2 . T . 99 . DP=89;VDB=0.0000;AF1=0.000;AFE=0.000;DP4=81,0,8,0;MQ=37;PV4=1,1,0.0005,1 P0
NC_002008 3 . T . 99 . DP=154;VDB=0.0000;AF1=0.000;AFE=0.000;DP4=101,0,0,0;MQ=36 PL 0
NC_002008 4 . A . 99 . DP=260;AF1=0.000;AFE=0.000;DP4=133,73,0,0;MQ=38 PL 0
NC_002008 5 . A . 99 . DP=262;VDB=0.0000;AF1=0.000;AFE=0.000;DP4=134,73,0,0;MQ=38 PL 0
NC_002008 6 . T . 99 . DP=263;VDB=0.0000;AF1=0.000;AFE=0.000;DP4=133,73,0,0;MQ=39 PL 0

I'm using the newest and the previous version of samtools. 0.1.18 and 0.1.19 like I wrote in my post. Bcftools and vcfutils come with samtools. So they all are up to date.

Thanks,
Stefan
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