Samtools consensus sequence error

[figo1019]

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

[TiborNagy]

I think your aln.bam file has some missing columns.

[figo1019]

I think your aln.bam file has some missing columns.

Thank you for your reply.
1.Please let me know why it can happen as I can generate 10 chromosomes in the consensus file and then it gives the error but i can see all the chromosomes in the bam files with the number of reads mapped.
2.How i can check in the bam file if that column is missing.

Regards

[TiborNagy]

Well, I can imagine a lots of scenarios. For example the aln.bam was concatenated from more than one file.
You can simply check the number of columns with the following command (in Unix/Linux):
samtools view aln.bam | awk -F"\t" '{print NF}'
or you can use tee command. It is write the pipe to file and the stdout at the same time. Good for debugging.