How to handle heterozygous INDELS

[volavii]

Hey,

how do you handle INDELS which show in a .vcf file a heterozygous status. Meaning there are two alleles in the sample: 50% of the reads show the INDEL the remaining ones do not show this INDEL. Do you know what is the general procedure for these cases? Or does someone knows a nice paper handling/discussing this case?
I want to create a consesus sequence from my mapping data, but I`m usure on what to do with these specific INDELS.

MANY THANKS IN ADVACE!

Volavi

[Melissa]

If I were to do this, I would store the consensus sequences in a pileup format. You might get better ideas after looking at SOAPindel and indelrealigner.

http://soap.genomics.org.cn/soapindel.html

https://www.broadinstitute.org/gatk/...ealignment.pdf

[volavii]

Hey,

thanks for your reply. I already used the indelrealigner and further steps were done by GATK-tools, too. But there are still heterozygous INDELS and I need a consensus sequence for furhter steps.... My Idea was to have both, consensus and the INDEL-vcf to be later able to check if a specific region of the genome - which is under investigation - may contains two different alleles (INDEL and no INDEL)....

Thanks,
volavii