SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
genotype in the output file of bcftools pengchy Bioinformatics 2 03-24-2012 10:52 AM
Compare 2 file genotype poca Bioinformatics 0 11-15-2011 12:58 AM
samtools Option to get genotype likelihood (GL) hansdd Bioinformatics 7 11-01-2011 06:04 AM
genotype calling conversion johnsequence Bioinformatics 0 10-31-2011 08:16 AM
genotype info from MAQ johnsequence Bioinformatics 0 10-28-2011 06:43 PM

Reply
 
Thread Tools
Old 03-26-2012, 08:10 PM   #1
plantae
Junior Member
 
Location: china

Join Date: Dec 2010
Posts: 7
Default genotype likelihood inconsist with genotype field in mpileup output

hi, all
I call SNPs using mpileup from samtools, I got strange results like:

Gm01 2923425 . A G,C 999 . DP=308;VDB=0.0224;AF1=0.6;G3=0.4,1.742e-06,0.6;HWE=0.00948;AC1=8;DP4=46,45,111,93;MQ=55;FQ=999;PV4=0.61,1,4.6e-0
9,1 GT:PLP:SP:GQ 1/1:255,157,0,255,157,255:52:0:99 0/1:255,255,255,169,169,0:56:0:3 0/0:200,255,255,0,255,255:59:2:48 1/1:255,102,0,255,102,25
5:34:0:99 0/0:0,154,255,154,255,255:51:0:99 0/1:255,255,255,90,90,0:30:0:3 1/1:255,39,0,255,39,255:13:0:37

According VCF format specification:
http://www.1000genomes.org/wiki/Anal...mat-version-41

the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc.

However, in my case, for example,
GT:PLP:SP:GQ 0/1:255,255,255,169,169,0:56:0:3
the six field from PL string has the lowest value-"0", thus the genotype might be CC, so the GT field should be 1/1, but I get 0/1 in this case.

another example:
0/0:200,255,255,0,255,255:59:2:48
the forth field was "0", thus genotype might be A/C, and GT field must be 0/1, I get 0/0 in this case.

I am confused about this.
plantae is offline   Reply With Quote
Reply

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 12:46 AM.


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