Question: Samtools Mpileup Error In Making The Consensus Sequences
1
gravatar for figo
6.7 years ago by
figo200
figo200 wrote:

Dear All

I am trying to make consensus sequences using command

samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq.

But i am getting this error:

[bcf_sync] incorrect number of fields (4 != 5) at 15:16294867
[afs] 0:49470.732 1:50.052 2:33.216

Can some one help me to sort out this problem. What exactly is going wrong.

Regards

samtools mpileup • 2.4k views
ADD COMMENTlink modified 6.7 years ago by Rm7.9k • written 6.7 years ago by figo200
2
gravatar for Rm
6.7 years ago by
Rm7.9k
Danville, PA
Rm7.9k wrote:

Follow this thread at seqanswers:

ADD COMMENTlink written 6.7 years ago by Rm7.9k
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