I am using the newest version of samtools and bcftools (Version: 1.2 (using htslib 1.2.1)) to call the snps from sorted Bam files, but I have error all the time. I try to search online, but no clear answer about this, Could anyone can help me to figure out this?
this is the commands what I used:
[wu@correns RMR1_subsample_1000000]$ samtools mpileup -uf BRP.fas RMR1_sub_1000000_1_mit.sort.bam RMR1_sub_1000000_2_mit.sort.bam | bcftools view -vcg - > BRP.Chr01.vcf
[mpileup] 2 samples in 2 input files
<mpileup> Set max per-file depth to 4000
[E::cg] unknown type
I try to different computers and still met the error.