Samtools consensus sequence error

[figo1019]

Dear All

I am again posting this question to the Bioinformatics forum as I didn't get the answer from the Illumina forum.

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

[Torst]

The issue seems to be in the "bcftools" step in your pipe ie. [bcf_sync].

Googling suggests two things:

1. there was an bug in previous bcftools when using "-" stdin, so maybe you have an old bcftools.

2. this occurs when you have indels, so try the mpileup "-I" option to not call indels and see if the error still occurs.

[figo1019]

The issue seems to be in the "bcftools" step in your pipe ie. [bcf_sync].

Googling suggests two things:

1. there was an bug in previous bcftools when using "-" stdin, so maybe you have an old bcftools.

2. this occurs when you have indels, so try the mpileup "-I" option to not call indels and see if the error still occurs.

Dear Torst

Thank you for your reply.

1. I am using the samtools 0.1.18 version.
2. I tried what you suggested and I didn't get the error this time but it again stops at the same point and I miss the same no. of chromosomes in the consensus sequence file e.g. when use grep to count the no. of chr in the .fq file I find the few chromosomes missing which was the same with the error also.

Regards