The command line you are using refers to the older version of bcftools (v.0.1.19). The -b option is deprecated in new bcftools (v.1.1), which you are using.
I have not tested the following command line. See if it works for you.
PS: If you type
Then that should print the help for the bcftools view command. You can then choose the appropriate command line options for various parameters.
I have not tested the following command line. See if it works for you.
Code:
$ samtools mpileup -uf /example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -O u -v -c 5 -g hom - > eg2.raw.bcf
Code:
$ bcftools view
Comment