Hi,
the commands are obsolete, please see here instructions for the
recommended workflow:
http://samtools.github.io/bcftools/howtos/variant-calling.html
Best wishes,
Petr
On 05/07/2020 20:47, White, Noor (NIH/NEI) [F] via Samtools-help wrote:
Hello,
I am repeatedly getting the below error running samtools (v1.10) and
python (v3.7, though I get the same error when I re-run with python
v2.7). I do not believe the error has to do with my SAM-format output,
original sample or query reference, as I have switched all out. I
found some similar error messages online, but no resolution. Thanks in
advance for any possible help.
Command:
samtools mpileup -Q 20 -q 5 -d 5000 -uf Ggal_exon_sequences.fasta
Mapped_AG_WGS_Ggal_exon.bam | bcftools call -c | vcfutils.pl vcf2fq -d
5 -Q 20 -l 1 >Consensus_AG_WGS_Ggal_exon.fq
Error:
Use of uninitialized value $l in numeric lt (<) at
/usr/local/apps/samtools/1.10/bin/vcfutils.pl line 566, <> line 412.
--
Noor D. White, PhD
/Postdoctoral Fellow/, National Science Foundation
/Postdoctoral Fellow/, National Eye Institute, National Institutes of
Health
/Research Collaborator/, National Museum of Natural History,
Smithsonian Institution
NNRL [nei.nih.gov]
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National Eye Institute [nei.nih.gov]
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NIH [nih.gov]
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