I'm using samtools/1.2 and bcftools/1.2
I'm having the similar issue with https://github.com/samtools/bcftools/issues/50 : (non of the replies solves my problem...)
samtools mpileup -uf ref.fa my.bam | bcftools call -c - | vcfutils.pl vcf2fq > my.fq
I'm getting all nnnnnnnnn and !!!!!!!!!!!!!!!!!! in the final fq file.
Is this something wrong with "vcfutils.pl" itself? I googled around, it seems people have same question, but no solution.
How can I get a correct fast file now?
P.S. Besides vcfutils.pl, I did try bcftools consensus, it worked fine for me. But my problem is, in my bam file, there are supposed to be some missing data. Since the consensus sequence was mapped to human reference genome, I guess all the missing/low quality sites are taken as the same as human reference genome? (even if this works, dead-end? and I have the vcf file I want, I don't need to generate them from bam file by myself.)
Thanks a lot!!!