How do I go about converting a BCF file to a VCF file?

[Giffredo]

samtools mpileup -f .fas .sorted.bam > .bcf | bcftools view > .vcf&

Just now I have used

samtools mpileup -f .fas .sorted.bam | tee teeoutput.bcf&

This "artefact" maybe works..

[TiborNagy]

Can you share us the command line?

[Giffredo]

I have the same problem but I have not "seen" yet ...

i want to use mpileup without -u and -g options but all the command line used did not work..

[prs321]

Ahh I see i see, thanks.

[westerman]

Every example? How about http://samtools.sourceforge.net/mpileup.shtml. One of my first hits via Google.

However what you are probably overlooking is the proper command line option to mpileup. Either look at the above web page and/or type in 'samtools mpileup' and read the help or look at your output file. It will be good for your eyes to spot the mistake. :-)

[prs321]

I tried using BCFtools but I keep getting an error.



1. I had 2 SAM files that converted to BAM, sorted by chromosome, and finally indexed using Picard.




2. Using the 2 manipulated BAM files, I used the mpileup command in SAMtools. Here is the specific command:

samtools mpileup -f ref.fa in.bam in2.bam > in_in2_pileup.bcf




3. After this step I wanted to get the vcf format. I used bcftools and the command view in order to do this:

bcftools view in_in2_pileup.bcf > in_in2_pileup.vcf


The error that I received after executing this command:

incorrect number of fields (0 != 5) at 0:0






PS. I tried looking my problem up in google search and every example seemed to be irrelevant in my case.