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# Haploid genomes

Member Posts: 19
edited July 2012

Dear GATK team,

I know that in the past GATK was not suitable for haploid genomes.
I wanted to ask if this possibly changed since then - and whether it is possible to use GATK for haploid genomes.

Thanks a lot,
Gilgi

Post edited by Carneiro on
Tagged:

The ug in gatk2 can call haploid sequence natively now. You just set ploidy to 1.

--
Mark A. DePristo, Ph.D.
Co-Director, Medical and Population Genetics
Broad Institute of MIT and Harvard

The ug in gatk2 can call haploid sequence natively now. You just set ploidy to 1.

--
Mark A. DePristo, Ph.D.
Co-Director, Medical and Population Genetics
Broad Institute of MIT and Harvard

• Member Posts: 19

Thanks! This is great news! I'll try to work with it.

• Member Posts: 19

Hi,

But after download saw that the version doesn't seem to be 2 but: version 1.6-596-g3b9929c

Is this the correct version?

Thanks,
Gilgi

The 2.0 release should be coming out later today.

Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

• Member Posts: 19

When trying to use the UnifiedGenotyper with --sample_ploidy 1 I get an error:
MESSAGE: Incorrect genotype calculation model chosen. Only [POOLSNP|POOLINDEL|POOLBOTH] supported with this walker if sample ploidy != 2

What does this mean? My data isn't pool, I have individual (barcoded) haploid sequenced strains.
--genotype_likelihoods_model POOLBOTH

But then I get:
MESSAGE: Incorrect AF Calculation model. Only POOL model supported if sample ploidy != 2

I tried to look for the answer in the guide - without success.

• Member Posts: 19

Thanks a lot!!!

• Member Posts: 1

Ive used the -pnrm POOL option but still getting the same error as gilgi. So I have

java -Xmx30g -jar /usr/local/gatk2/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ref -I bam -I bam -pnrm POOL -polidy 1 -o vcf

Any help?
Ali

We have changed the arguments so that they more accurately reflect what they are doing:
So you'll want e.g. -pnrm GeneralPloidySNP

Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

• Member Posts: 14

With v2.0-39 I had been using -ploidy 1 -pnrm POOL -glm POOLSNP. Can you confirm that for calling of snps/indels in haploid genomes as of v2.1 would now be -ploidy 1 -pnrm EXACT -glm GeneralPloidySNP. Is the -pnrm POOL option now defunct?

You just need -ploidy 1. "-pnrm EXACT" will work but there's no other option . "-glm GeneralPloidySNP" will not work - you need either SNP, INDEL or BOTH.

• Member Posts: 14

Thanks for your reply. Under what circumstance should -glm GeneralPloidySNP/GeneralPloidyINDEL be used?

• Member Posts: 3

I am experiencing a problem with the ploidy 1 option.
Having used GATK2 unified genotyper with the params --sample_ploidy 1 --genotype_likelihoods_model BOTH -rf BadCigar
I get the following line in a vcf file (see sample in bold)

Staphylococcus 1553115 . A G 24454.01 . AC=13;AF=0.813;AN=16;BaseQRankSum=1.072;DP=1040;Dels=0.00;FS=32.822;HaplotypeScore=3.3463;MLEAC=13;MLEAF=0.813;MQ=40.20;MQ0=47;MQRankSum=-10.543;QD=32.13;ReadPosRankSum=-1.148;SB=-9.076e+03 GT:AD:DP:GQ:MLPSAC:MLPSAF:PL 1:0,29:29:99:1:1.00:1015,0 1:0,62:62:99:1:1.00:2053,0 1:0,106:106:99:1:1.00:3210,0 1:0,102:102:99:1:1.00:3305,0 1:0,88:88:99:1:1.00:2750,0 1:0,41:41:99:1:1.00:1324,0 1:0,76:76:99:1:1.00:2448,0 1:0,39:39:99:1:1.00:1303,0 0:64,40:104:99:0:0.00:0,1334 1:0,41:41:99:1:1.00:1373,0 1:0,49:49:99:1:1.00:1668,0 0:72,50:122:99:0:0.00:0,1258 1:0,59:59:99:1:1.00:1852,0 1:0,38:38:99:1:1.00:1192,0 1:0,31:31:99:1:1.00:961,0 0:53,0:53:99:0:0.00:0,1633

The sample in bold is called as WT (genotype 0) with a high GQ despite there being 72 reads of genotype 0 and 50 of genotype 1. Examining the bam file suggests that this is a mapping error in a repetitive phage region

If I set ploidy to be 2 the equivalent line in the resulting vcf file is

Staphylococcus 1553115 . A G 24788.02 . AC=28;AF=0.875;AN=32;BaseQRankSum=0.947;DP=1040;Dels=0.00;FS=32.822;HaplotypeScore=3.3463;InbreedingCoeff=0.4286;MLEAC=28;MLEAF=0.875;MQ=40.20;MQ0=47;MQRankSum=-10.096;QD=25.11;ReadPosRankSum=-1.177;SB=-9.871e+03 GT:AD:DP:GQ:PL 1/1:0,29:29:81:986,81,0 1/1:0,62:62:99:1895,156,0 1/1:0,106:106:99:2992,247,0 1/1:0,102:102:99:3169,268,0 1/1:0,88:88:99:2452,193,0 1/1:0,41:41:99:1243,99,0 1/1:0,76:76:99:2283,193,0 1/1:0,39:39:99:1233,105,0 0/1:64,40:104:99:886,0,1706 1/1:0,41:41:99:1298,108,0 1/1:0,49:49:99:1581,129,0 0/1:72,50:122:99:1235,0,2126 1/1:0,59:59:99:1649,132,0 1/1:0,38:38:87:1065,87,0 1/1:0,31:31:69:821,69,0 0/0:53,0:53:99:0,138,1588

As can be seen from the bold text, the same position is called as heterozygote which based on the number of the reads mapping would be likley except for the fact this is a bacterial haploid genome. Previously I would have discarded this since the heterozygous call indicates mis-mapping as the bam file confirms. I had been hoping to use the sample_polidy option set to 1 for bacterial genomes but this results concerns me. I could obviously filter based on AD but the wonder why the sample was given a high GQ when the polidy is set to 1 and the AD suggests the call of genotype 0 should be doubted.

Any suggestions on what is going on here?? Many thanks

Anthony

The code is actually doing what it's designed to do - when you're using -ploidy 1, there are only 2 possible genotype assignments, and the assignment "0" is by far the most likely one even if 40% of your reads have another base. In the default diploid case, the most likely genotype is the 0/1 one, which is exactly what you're getting.
Even in the haploid case, there's considerable evidence that favors the "0" genotype (plus the population prior), so you'll get a high value of GQ anyway - your PL values of 0,1258 indicate that, statistically, it's 10^125 likelier that your data came from a reference site than from an alt site based on all the available reads.

• Member Posts: 14
edited January 2013

In the current documentation (v2.3-9) for the Unified Genotyper there is a caveat stating "We only handle diploid genotypes". Has something changed or can -ploidy still be safely set to 1?