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
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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