Question: remove primer sequences from BAM file
gravatar for J.F.Jiang
12 weeks ago by
J.F.Jiang720 wrote:

Hi all,

I am dealing with amplicon data, which was obtained from multiplex PCR.

Original primers can largely increase the mapping accuracy, since some amplicons are highly homologous with little difference within primer region.

And since these primers may introduce FAKE SNPs when they are within inserted regions from other amplicons, we want to remove the primers from BAM file. can clip the primer sequence, however, it is time-consuming when amplicon is sequenced more than 1000X.

GATK can softly clip the sequence. However, it can also clip the sequence that is similar with the primers, especially those are not the real primers, but the insert sequence.

I am wondering if there is any tool that can quickly clip the real primers.

Best, Junfeng

primer bam • 242 views
ADD COMMENTlink written 12 weeks ago by J.F.Jiang720

An alternative solution would be to use the -L argument of GATK to specify variant calling to a certain region (bed file) within the amplicons, excluding the primers.

ADD REPLYlink written 12 weeks ago by WouterDeCoster34k


Take the scenario above as consideration, if position * is always T, but C in the primer region of the second amplicon. The calling result will give T/C SNP, however, the C allele is just the PCR error or synthesis error. If we remove the primer sequence of the amplicons, the final calling will be T/T as expected.

ADD REPLYlink modified 12 weeks ago by WouterDeCoster34k • written 12 weeks ago by J.F.Jiang720

Oh, so you mean you have overlapping amplicons? Right... then my suggestion doesn't work.

ADD REPLYlink written 12 weeks ago by WouterDeCoster34k

yes, -L option can handle with non-overlapped regions.

ADD REPLYlink written 12 weeks ago by J.F.Jiang720
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