Filtering Pcr Duplicates In Mpileup

Question

[Les Ander]

Hi, I'm using samtools 0.1.17. While there is an option to filter out duplicates using samtools view, I don't see an option in mpileup to do this. Does anyone know how I can get mpileup to ignore PCR duplicates (flag 0x400) thanks Les

Answer 1

[Zhidkov]

Hi, mpileup parses BAM file, before you running "samtools mpileup", sort your file "samtools sort", then remove PCR duplicates "samtools rmdup", then run the mpileup. Ilia

[Les Ander]

Hi zhidkov, Thanks for the response. I can certainly create a bam file without the pcr duplicates (using samtools view -F 0x400) --but that would waste space. I was looking for a way to do this in mpileup without having to create a new bam file. thanks