My question is does samtools mpileup automatically removed duplicates from test.marked.bam output from Picard/MarkDuplicates? Because I am not following any other step to remove duplicates.
I used Picard Tools to create: test.marked.bam
Then I use "samtools mpileup -uf test.marked.bam | bcftools view -bvcg -> test.marked.bcf "
"bcftools view test.marked.bcf | vcfutils.pl varfilter -D1000 >test.marked.vcf"
Thanks very much