bam to consensus sequence--error

[wuzhiqiang]

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

[nq1027]

Hi, do you solve this problem? I meet this problem too. Can you please tell me what is wrong? Thank you very much!

Regards

Kimi

[GenoMax]

With the new release of bcftools (v.1.x) the default options have changed. You have to provide a numeric argument for -c option.

-c/C, --min-ac/--max-ac <int>[:<type>] minimum/maximum count for non-reference (nref), 1st alternate (alt1) or minor (minor) alleles [nref]