Question: (Closed) Samtools (Bcftools) Error Regarding Fields For Mpileup
gravatar for Jlw
6.5 years ago by
Jlw180 wrote:

Been struggling with a new error that has popped up with calling variants with samtools, using mpileup

Current command:

samtools mpileup -C50 -Q 20 -q 20 -B -I -S -f ../Pila.88.seeds.fasta pila.s1.sort.nodup.bam pila.s2.sort.nodup.bam pila.s5.sort.nodup.bam | bcftools view -bvcg - > pila.var.raw.bcf


[mpileup] 3 samples in 3 input files
<mpileup> Set max per-file depth to 2666
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
[afs] 0:0.000

I have tried stripping everything down to one bam file, no specific parameters but it's always the same error. The bam files themselves are fine, not corrupted as I was able to sort, index, etc without issue. I did perform a conversion from sam to bam following a bwa mapping step and perhaps that could be a problem. The conversion was performed in samtools with view however and this was repeated again to ensure no errors come from there.

I just pulled the latest code as posts indicate issues similar to this have been resolved...

samtools bcftools snp mpileup • 4.1k views
ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Jlw180

Could you run Picard ValidateSamFile on your bam-alignment and post what that says?

ADD REPLYlink written 6.5 years ago by Philipp Bayer6.3k
gravatar for Jlw
6.5 years ago by
Jlw180 wrote:

Found the error in my ways. Missed a very critical -u flag in the mpileup line to produce the uncompressed bcf.

ADD COMMENTlink written 6.5 years ago by Jlw180
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