Question: samtools mpileup: bam file to consensus sequence generation error?
0
gravatar for Dineshkumar K
10 months ago by
Kasaragod, Kerala, India
Dineshkumar K40 wrote:

I have been doing reference based assembly of illumina based paired end reads. For which, I indexed my reference genome and generated sam, bam and sorted.bam files, further proceeded for consensus sequence generation using the following command,

samtools mpileup -uf reference.fasta query.sorted.bam | bcftools view -cg - | perl vcfutils.pl vcf2fq | seqtk seq -A -l 70 - | sed -r "s/(>)(.*)/\1 query.bam.consensus/g" > consensus.fasta

and end up with error as follows,

Error: Could not parse --min-ac g
Use of uninitialized value $l in numeric lt (<) at vcfutils.pl line 566.
Use of uninitialized value $l in numeric lt (<) at vcfutils.pl line 566.
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

The strange thing is that, the same command line is working well (without showing error) in ubuntu 14 and 16 LTS OS version, but showing above mentioned error in ubuntu 18 LTS OS version. Please help me to fix this issue.

ADD COMMENTlink written 10 months ago by Dineshkumar K40

There is an issue on github related to his https://github.com/samtools/bcftools/issues/391

ADD REPLYlink written 10 months ago by microfuge1.7k
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