Hi Everyone. I used samtools mpileup to call SNPs and indels. I got the same number of SNPs when
(1) using "samtools mpileup -ugf a.bam"
and
(2) first use "samtools view -bq 1 a.bam > clean.bam", then use "samtools mpileup -ugf clean.bam"
Is this reasonable? The total number of reads in a.bam and clean.bam is apparently different (using samtools flagstat to check). I wonder why I got the same results. Did I miss something?
I also checked "-bq 15". Strangely, I got a little bit more SNPs than using "-bq 1". Can anyone share some comments on this? Is there any suggestion on the parameter "-q"?
Thanks!
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