CombineVariants: AD field not updated when merging variants with different REF and ALT alleles
Posted in Ask the team | Last updated on 2012-10-03 18:01:31

Comments (5)

When I run CombineVariants on two vcf files with variants at the same position but with different REF alleles and also different sets of ALT alleles, the AD fields for the genotypes are not updated to reflect the changes in the ALT field. The REF and ALT fields and the GT field for each genotype are all correctly updated. For example combining

3   10128965    rs71052293  CTT CT,C,CTTT   19936.43    PASS    AC=1,1,1;AF=0.25,0.25,0.25;AN=4 GT:AD:DP:GQ:PL  0/2:115,0,33,12:230:6.96:980,1237,2795,0,946,1900,7,679,467,817 3/1:97,13,20,16:229:99:804,221,832,581,176,3047,521,0,1653,1595


3   10128965    rs71052293  CT  C,CTT,CTTT  14280.61    PASS    AC=1,1,1;AF=0.25,0.25,0.25;AN=4 GT:AD:DP:GQ:PL  2/1:110,20,33,18:237:1.90:850,289,1027,457,0,1487,147,877,2,1858    0/3:80,48,5,29:209:99:1835,875,977,2101,1119,3322,0,142,331,462


3   10128965    rs71052293  CTT CT,C,CTTT,CTTTT 19936.43    PASS    AC=2,1,2,1;AF=0.250,0.125,0.250,0.125;AN=8;set=Intersection GT:AD:DP:GQ 0/2:115,0,33,12:230:7   3/1:97,13,20,16:229:99  3/1:110,20,33,18:237:2  0/4:80,48,5,29:209:99

There five alleles (one REF and four ALT) but only four AD fields for each genotype.

My command line:

java -jar -Xmx4g GenomeAnalysisTK.jar -T CombineVariants -R human_g1k_v37.fasta -V test_input1.vcf -V test_input2.vcf -o test_combined.vcf

Is this a known limitation or a bug?

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