Hello,
I have a problem to use mpileup. I used this command:
samtools mpileup -f mi.fas sorted.bam > X.bcf &
bcftools view X.bcf > X.vcf &
it doesn't work "incorrect number of fields (0 != 5) at 0:0". I d like to optain vcf output from bam without using -u and -g in order to reach the result described in the manual http://samtools.sourceforge.net/samtools.shtml
If I try
samtools mpileup -f mi.fas sorted.bam > 2eccolo.bcf | bcftools view > 2eccolo.vcf&
It works but the results is an empty table...
P.S. using only the line below, it did not give me an output; I see only the results print on screen...
samtools mpileup -f mi.fas sorted.bam&
•
written
by
Giffredo •
The command you're looking for is tee
samtools mpileup -f mi.fas sorted.bam | tee X.bcf | bcftools view - > 2eccolo.vcf
or something like that.
Edit: I just realized that you're not outputting BCF in the first place, just mpileup, which is text! That won't ever work. You'll need to use the -g or -v or similar.
Unfortunately it doesn t work.. it gives me the same error incorrect number of fields (0 != 5) at 0:0 Anyway tee is a good idea! thanks!
Oh, I just noticed that you didn't use -g or -u or similar and updated my answer, since that won't work.
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