BCFtools outputs error : [bcf_sync] incorrect number of fields (6 != 5)
I launched samtools to call SNPs on 2 BAM files, and when it comes to BCFtools, both returned an error.
$ samtools mpileup -ugf refseq.fa aln.bam | bcftools view -bvcg - > var.raw.bcf
$ bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf
It returns the following error:
[bcf_sync] incorrect number of fields (6 != 5) at 13:51289753
What does it mean? Can I just skip this error and keep going with my list of SNPs and indels?
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Did you use
nohupsomewhere in your unix command?No I didn't use nohup, what does it stand for and what does it do? I figured that error happens when the BCF file is truncated .. now I'm not sure why it's truncated yet
Is it matter if I use the
nohupcommand ? I have met a similar problem as the error isThe following is the command that i have used to generate BCF file:
I have got an possible answer here:
And without using the
nohupmy file works fine.