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how to get low depth variants in vcf file (hetrozygous condition)

I want to get a variant in vcf file which is present in hetrozygous condition. for example if at a specific position 50 reads get mapped and 26 of them are same as reference and 24 reads have an alternate allele. that specific position didn't show up as variant in vcf file. But I want them in vcf file as they are very important to me. How can I do that ???

snp next-gen alignment
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updated by Biostar Biostar • written by hafiz.talhamalik hafiz.talhamalik

how did you get that vcf ? which tool ? what are the MAPQ of those reads ?

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written by Pierre Lindenbaum Pierre Lindenbaum

I used SAMTOOLS for variant calling and for filteration I used mapping quality greater then 20

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written by hafiz.talhamalik hafiz.talhamalik

50 reads is not "low depth" IMHO. Can you please send us a IGV view of the region.

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written by Pierre Lindenbaum Pierre Lindenbaum

Hello hafiz.talhamalik!

We believe that this post does not fit the main topic of this site.

OP never followed up.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

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