Question: Multiple SNPs within few bases
gravatar for Chirag Nepal
2.9 years ago by
Chirag Nepal2.0k
Chirag Nepal2.0k wrote:

Hi There,


Some of the predicted somatic snippers are close, 2/3 SNPs within 10 nt window.

Varscan actually filters such SNPs when using their filtering scripts.

So SNPs that are close to each other, or close to indel, why are such SNPs discarded. If i want to filter such SNPs using some distance, what distance, 10nt or 20nt, what might be appropriate.


Thanks !


snp somaticsniper varscan • 692 views
ADD COMMENTlink written 2.9 years ago by Chirag Nepal2.0k

Usually, if multiple snps are observed in a short distance e.g. 1 read length, then it is very likely there is an indel in the area and you should try to first  perform the local realignment before calling.

ADD REPLYlink written 2.9 years ago by Sam2.1k
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