Hi everyone,

I am trying to make a consensus from a aligned bam file.
This is my workflow:

    bcftools mpileup -Ou -f reference_HG19.fa aligned.bam | bcftools call -mv -Ob -o calls.bcf
    
    bcftools index calls.bcf
    
    cat reference_HG19.fa | bcftools consensus calls.bcf > consensus.fa

However, the created consensus.fa file turned out to be identical with the reference_HG19.fa file.
I looked at calls.bcf file with bcftools view, and it seems the following columns are all empty:

    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT aligned.bam

When I look at calls.bcf with samtools view I get the error "Aborted".

Does anyone have an idea how to solve this issues? 
Thank you very much!

Robert
We finally found the solution:
The downloaded `bam` was generated by paired end sequencing. For some unknown reason `bcftools` considers these read pairs to be "anomalous". By using the `-A` input option one prevents `bcftools` from skipping anomalous read pairs. Now it's working as it is supposed to. 
