Hi I have used the below command line to call SNPs: samtools-1.2/samtools mpileup -q 25 -Iu -f reference.fasta .*.sorted.bam | bcftools view -Nv - | vcfutils.pl varFilter -Q 20 - >multicall.vcf
but it gives the following error:
[mpileup] 20 samples in 20 input files [bcf_sync] incorrect number of fields (0 != 5) at 0:0 [afs] 0:0.000
and the vcf file it generated only has the headers
Please give any suggestions which will help a lot!! I have been stuck on this for so long...