Allele information in IGV

[Sini]

Hello,

I called variants from a tetraploid Drosophila sample and have visualised the vcf file in IGV. However, I don't understand how the information displayed in the Alleles section in the pop-up window for each SNP is derived. Please see attached three screenshots from different examples. The first example is a SNP, which is homozygous for the alternative allele, and it has Allele Num 2, Allele Count 4 and Minor Allele Fraction 1. In the second example is a SNP with an alternative allele frequency of 0.25. Here the Allele Num is 2, Allele Count is 2 and Minor Allele Fraction is 0.5, although Allele Frequency is 0.25. The third example is a SNP with two alternative alleles. The other alternative allele has a frequency of 0.25 and the other 0.75, which are displayed in Allele Frequency, but Allele Num is 2, Allele Count is 2 and Minor Allele Fraction is again 0.5.

Can you explain to me how these numbers are calculated? At the moment they don't seem to make any sense.

Thank you,
Sini

[Jim Robinson]

Hi,

In general those numbers are not calculated by IGV, they are just read from the VCF file.

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[Sini]

Hi,

the SNP calling was done with GATK and I already asked them about this, but they said to contact you.

Here are the VCF records for the SNPs represented in the examples:

2L 2500475 ENSVDME00144720 A T 560.24 PASS AC=4;AF=1.00;AN=4;DB;DP=15;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=60.00;QD=24.80;SOR=1.863 GT:AD:DP:GQ:PL 1/1/1/1:0,14:14:20:559,96,48,20,0

2L 2500243 . C T 134.2 PASS AC=1;AF=0.250;AN=4;BaseQRankSum=-0.464;ClippingRankSum=0.689;DP=42;FS=1.492;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.368;QD=3.20;ReadPosRankSum=2.194;SOR=1.030 GT:AD:DP:GQ:PL 0/0/0/1:34,8:42:36:161,0,36,124,994

2L 2499895 ENSVDME00144668 A G,T 1997.2 PASS AC=1,3;AF=0.250,0.750;AN=4;DB;DP=54;FS=0.000;MLEAC=1,3;MLEAF=0.250,0.750;MQ=58.28;QD=29.77;SOR=1.251 GT:AD:DP:GQ:PL 1/2/2/2:0,2,45:47:74:2024,1883,1891,1918,2120,371,219,213,215,233,81,74,152,0,95

The values in the Variant Attributes section in IGV pop-up window match the values in the VCF file, but the Allele Num, Allele Count and Minor Allele Fraction values in the Alleles section in IGV do not seem to match the VCF file. Also the bars visualising the SNPs are coloured according to the Minor Allele Fraction value, is there a way to colour them according to the Allele Frequency?

Regards,

Sini

[Jim Robinson]

Oh sorry,  I misunderstood.   I'll look into this.

Jim

On 2/11/16 12:13 AM, Sini wrote:

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[Jim Robinson]

Hi,  I'm looking into this now, sorry for the delay.   It looks like there is an assumption of  ploidy=2, which might account for some of the discrepancy.   Would it be possible to attach the header to the VCF file for the records shown?  I would like to construct a test case using these, and need the header to properly parse the records.

Thanks

Jim

[Sini]

Hi,

here's the VCF header attached. 

Best,

Sini

[Jim Robinson]

Thanks.  This should be fixed now, in version 2.3.69.

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