Question: How can I label snp that are false positive?
0
gravatar for agata88
4.1 years ago by
agata88790
Poland
agata88790 wrote:

Hi all!

I am working on multiplex NGS results. I have vcf file which contains a lot of false positive variants. I know they are false positive because they obtain last nucleotide in read (from overlapping reads they are not present). I would like to label those variants. Do you know why I have those variants? I was performing primer trimming by cutadapt.

Those variants only appear in multiplex results. I don't see them in results created by probe (for the same sample).

Any idea?

PS. This could be caused by not performing "marking duplicates", but in multiplex it is impossible to do that.

Best,

Agata

multiplex ngs vcf • 1.3k views
ADD COMMENTlink written 4.1 years ago by agata88790

Depending on the variant caller you used, there may be an indicator already there of the bias due to read position. If so, you can filter/mark by that.

ADD REPLYlink written 4.1 years ago by Devon Ryan95k

I am using samtools mpileup to generate bcf files and then bcftools to create vcf files. Are those tools able to do that?

ADD REPLYlink written 4.1 years ago by agata88790

I know GATK at least used to determine this (the "ReadPosRankSumTest"), but I don't recall seeing samtools do it.

ADD REPLYlink written 4.1 years ago by Devon Ryan95k

Thank you very much, I'll try this :)

ADD REPLYlink written 4.1 years ago by agata88790
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