Hey,
My question is does samtools mpileup automatically removed duplicates from test.marked.bam output from Picard/MarkDuplicates?
I used Picard Tools to create: test.marked.bam
Then I use
"samtools mpileup -uf test.marked.bam | bcftools view -bvcg -> test.marked.bcf "
and
"bcftools view test.marked.bcf | vcfutils.pl varfilter -D1000 >test.marked.vcf"
Thanks very much
My question is does samtools mpileup automatically removed duplicates from test.marked.bam output from Picard/MarkDuplicates?
I used Picard Tools to create: test.marked.bam
Then I use
"samtools mpileup -uf test.marked.bam | bcftools view -bvcg -> test.marked.bcf "
and
"bcftools view test.marked.bcf | vcfutils.pl varfilter -D1000 >test.marked.vcf"
Thanks very much