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?