Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Haploid inspiration gibberwocky Bioinformatics 3 07-02-2014 06:29 AM
Consensus from mpileup for haploid sequences (forcing base calls - no ambiguities) ericarcher Bioinformatics 6 01-24-2014 08:52 AM
Homozygous Ref calls and no calls ashkot Bioinformatics 1 08-09-2012 10:01 AM
mpileup on haploid samples agc Bioinformatics 1 11-24-2010 04:14 AM
Is short-read sequencing a haploid or diploid sequencing? choyk1 General 1 06-02-2009 01:48 PM

Thread Tools
Old 07-07-2017, 01:47 AM   #1
Junior Member
Location: United states

Join Date: Jul 2017
Posts: 2
Lightbulb Diploid vs haploid calls

Hi everyone,

My question is a basic one, but very important to understanding how sequence processing actually works.

What determines (how does a variant calling program know) whether a specific locus in a sequenced dna fragment should be diploid (e.g A/T or C/G) or haploid (e.g C/C, T/T).

Is it based on what the reads are for that locus, for example, if at least 25% of the reads for that locus are C, and the remainder T, then the position will be called C/T, whereas if less than 25% of the reads are C, and > 75% of the reads are T, then the position will be called T/T (the 1 or 2 Cs will be discarded as sequencing errors)

or is it based on whether the human reference is diploid or haploid for that locus or a combination. Please give specific examples to illustrate how reads look for a diploid vs haploid call.


Last edited by Ghani; 07-07-2017 at 02:10 AM. Reason: Elaborate
Ghani is offline   Reply With Quote
Old 07-07-2017, 06:47 PM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,657

For reference cross-posted on Biostars:
GenoMax is offline   Reply With Quote

diploid calling, haploid calling

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 04:19 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO