Newbie to the bioinformatic area and looking for some help.
I'm trying to use bcftools to do some SNPs calling from a bcf file created out of "samtools mpileup".
In a lot of posts I see the bcftools view options as "-bvcg", but when I try it I get the error
bcftools: unknown option -- b
In reading I see that bcftools have changed their view options with the more recent versions (i'm runnning 1.2), so was wondering if any one can translate the old options into what to use for the new options values. I'm trying :-
"-O b -v snps -g het"
but since I have never used bcftools before I don't know if that would get me the same output.
Thanks for your assistance in advance.