Remove Duplicates from Illumina AmpliSeq data

Question

[preeti.singh]

Hi Everyone,

Could anyone please recommend any tools to remove duplicates from AmpliSeq paired-end data (not MarkDuplicates)? I am having a difficult time to find such tool. Any help is much appreciated. Please let me know if further details are required.

Thanks.

Best wishes,

Preeti

[finswimmer]

AmpliSeq is an amplicon based (pcr based) library method, isn't it? Unless you have used UMI, you have no chance to say which read is a pcr duplicate. So don't remove "duplicates", because as you said, you will end up having only 1 read per position.

[preeti.singh]

Thanks finswimmer.

As you suggested I will give it a go without removing duplicates and see how the VCFs look on IGV.

Preeti

[Pierre Lindenbaum]

not MarkDuplicates

why ?

[preeti.singh]

Hi Pierre,

In theory, MarkDuplicates and/or rmdup will remove all reads. In Ampliseq, DNA is fragmented after the target is captured so most of the reads could possibly be from same DNA fragment, also ion Torent suggest not to remove duplicates. So was wondering if any tool is specific for AmpliSeq reads.

Preeti

[gb]

Are it just fasta files?

VSEARCH --derep_fulllength

[preeti.singh]

No on aligned bam files (after conversion of aligned SAM files)