Hi,
When I use samtools mpileup, I get bases with base qualities lower than the -Q cutoff. For example my command
$samtoolsdir/samtools mpileup -f $resdir/human_g1k_v37.fasta my_reads.recal.bam > junk.pileup
should have the default cutoff of 13, but I see bases with quality 2=# like
1 10257 A 1 . #
Setting -Q to something stupid like 200 seems to have no effect. I am using samtools-0.1.12a . Is there a way to filter output using quality in mpileup?
Thanks,
Vince
When I use samtools mpileup, I get bases with base qualities lower than the -Q cutoff. For example my command
$samtoolsdir/samtools mpileup -f $resdir/human_g1k_v37.fasta my_reads.recal.bam > junk.pileup
should have the default cutoff of 13, but I see bases with quality 2=# like
1 10257 A 1 . #
Setting -Q to something stupid like 200 seems to have no effect. I am using samtools-0.1.12a . Is there a way to filter output using quality in mpileup?
Thanks,
Vince
Comment