Tagged with #allelebalance
1 documentation article | 0 announcements | 3 forum discussions


Comments (0)

A new tool has been released!

Check out the documentation at AlleleBalance.

No posts found with the requested search criteria.
Comments (7)

Hi Team!

I have an issue that I'm not sure how to solve. I'm using HaplotypeCaller with a three member family and I have some calls when the HOM/HET call doesn't match with what we expected:

chr1 94487191 . A T 93.13 . AC=1;AF=0.167;AN=6;BaseQRankSum=-0.540;ClippingRankSum=-0.374;DP=87;FS=4.946;MLEAC=1;MLEAF=0.167;MQ=61.11;MQ0=0;MQRankSum=-0.042;QD=7.16;ReadPosRankSum=-0.042;set=GATK GT:AD:GQ:PL 0/0:40,0:99:0,102,2405 0/0:33,0:90:0,90,2215 0/1:11,2:99:124,0,760

In the third sample, the call is 0/1 (HET) but the coverage of each allele is 11 and 2, that means, with just 18% is considered as HET. There is a way to change the Allele Balance to 30%?

More info:

The Genome Analysis Toolkit (GATK) v2.5-2-gf57256b, Compiled 2013/05/01 09:27:02

Program Args: -T HaplotypeCaller -R ucsc.hg19.fasta -I S1.bam -I S2.bam -I S3.bam -o OUT.RAW.vcf --genotyping_mode DISCOVERY -stand_call_conf 30.0 -stand_emit_conf 10.0

Comments (1)

Hi Team,

I'm sequencing the genome of an organism which is a cross between the reference line (with no SNPs) and an individual from an outbred population (with many SNPs). Therefore all of the SNPs in my target organism will be heterozygous. So far I have sequenced three individuals which are crosses and one individual from our reference line.

I understand that the UnifiedGenotyper uses population genetic principles to ascertain genotype but I can't find more information about how this is performed. Thus, I am primarily worried that heterozygotes with strongly asymmetric allele counts in the reads will be called as homozygotes in order to fit in with, say Hard-Wienberg equilibrium.

Is there any chance you could enlighten me on this ? (or direct me to more detailed information on UG mechanism and settings).

Just to let you know the background, my study organism is Drosophila melanogaster. The whole genome of 164Mb is paired-end sequenced on an Illumina. I have so far sequenced one individual from our in-house reference line, and three individuals which are crosses of the reference line with a diverse, out-bred population. Average coverage is 30X. The 'crosses' are hemiclones in which recombination between the parental chromosomes is suppressed. I plan on sequencing 200 hemiclone individuals in which one haplotype will be shared between them (the reference gene) and the other haplotype will be diverse and unique to each line. As expected, I have identified a limited number of mutations in our in-house laboratory reference line compared to that of the assembly.

Any advice on how to best call genotypes in this unorthodox sample would be most appreciated.

Comments (1)

We are using the unified genotyper to create a vcf file. In the vcf file we see the info tags;

INFO=<ID=ABHet,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">

INFO=<ID=ABHom,Number=1,Type=Float,Description="Allele Balance for homs (A/(A+O))">

but when we look at the exported annotations

ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;QD=12.21

we only see ABHom not ABHet.