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Filtering Pcr Duplicates In Mpileup

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

mpileup pcr duplicates samtools
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updated by Zhidkov Zhidkov • written by Les Ander Les Ander

1 answer

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

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written by Zhidkov Zhidkov

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

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written by Les Ander Les Ander

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