Hi everyone,
I am trying to generate a consensus sequence from a bam file generate. I used the
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
and obtained the following error message:
Error: Could not parse --min-ac -g
[mpileup] 1 samples in 1 input files
Use of uninitialized value $l in numeric lt (<) at /usr/local/bin/vcfutils.pl line 566.
Use of uninitialized value $l in numeric lt (<) at /usr/local/bin/vcfutils.pl line 566.
<mpileup> Set max per-file depth to 8000
Does anyone know what might have gone wrong? Thanks,
Jim
I am trying to generate a consensus sequence from a bam file generate. I used the
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
and obtained the following error message:
Error: Could not parse --min-ac -g
[mpileup] 1 samples in 1 input files
Use of uninitialized value $l in numeric lt (<) at /usr/local/bin/vcfutils.pl line 566.
Use of uninitialized value $l in numeric lt (<) at /usr/local/bin/vcfutils.pl line 566.
<mpileup> Set max per-file depth to 8000
Does anyone know what might have gone wrong? Thanks,
Jim
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