Dear all,
I am trying to make consensus sequences using command
samtools mpileup -uf Sa.fas Sa.bam | ../bcftools-1.0/bcftools view -cg - | ../bcftools-1.0/vcfutils.pl vcf2fq > Sa_cns.fq
[mpileup] 1 samples in 1 input files
Error: Could not parse --min-ac g
<mpileup> Set max per-file depth to 8000
Use of uninitialized value $l in numeric lt (<) at ../bcftools-1.0/vcfutils.pl line 566.
Use of uninitialized value $l in numeric lt (<) at ../bcftools-1.0/vcfutils.pl line 566.
Can some one help me to sort out this problem? What exactly is going wrong.
Regards
ZQ
I am trying to make consensus sequences using command
samtools mpileup -uf Sa.fas Sa.bam | ../bcftools-1.0/bcftools view -cg - | ../bcftools-1.0/vcfutils.pl vcf2fq > Sa_cns.fq
[mpileup] 1 samples in 1 input files
Error: Could not parse --min-ac g
<mpileup> Set max per-file depth to 8000
Use of uninitialized value $l in numeric lt (<) at ../bcftools-1.0/vcfutils.pl line 566.
Use of uninitialized value $l in numeric lt (<) at ../bcftools-1.0/vcfutils.pl line 566.
Can some one help me to sort out this problem? What exactly is going wrong.
Regards
ZQ
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