Question: remove primer sequences from BAM file
gravatar for J.F.Jiang
5 weeks ago by
J.F.Jiang710 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 • 161 views
ADD COMMENTlink written 5 weeks ago by J.F.Jiang710

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 5 weeks ago by WouterDeCoster32k


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 5 weeks ago by WouterDeCoster32k • written 5 weeks ago by J.F.Jiang710

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

ADD REPLYlink written 5 weeks ago by WouterDeCoster32k

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

ADD REPLYlink written 5 weeks ago by J.F.Jiang710
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