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Why does HaplotypeCaller call heterozygotes when all reads are identical?
Hello, I've been exploring the vcf output from HaplotypeCaller-in-gVCF-mode, and I noticed that for some SNPs (37/~250K), HaplotypeCaller has called a heterozygote when according to the VCF, all the reads support either the reference or the alternative allele (90% of the time, it is when all reads support the alternative allele).
There are for fairly low-coverage sites (all < 10), although from exploring the data, it looks like "GQ" values are quite high (20+) and that they are all loci that have been phased by HaplotypeCaller.
Is HaplotypeCaller doing something smart here with the phasing to "recover" information that isn't in the raw sequences? I can't really figure out what that might be, but I'm also don't really know what is going on under the hood with physical phasing.
In case it matters, I am working with mosquito exome data, 150bp PE illumina reads, GATK 220.127.116.11, java 1.8.0_181. I've been following the Broad best practices pretty closely, although I haven't managed to figure out how to bootstrap base recalibration yet.
An example line from the VCF, with the individual of concern bolded (note that there are some bulks in here, and I think they might be exhibiting the same behavior, but so far I'm only looking a diploid single individuals):
NW_021837111.1 53637 . T G 107.95 . AC=1;AF=9.434e-03;AN=106;DP=221;ExcessHet=3.0103;FS=0.000;InbreedingCoeff=-0.1312;MLEAC=1;MLEAF=9.434e-03;MQ=60.00;QD=32.06;SOR=2.833GT:AD:DP:GQ:PGT:PID:PL:PS 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:55,0:55:8:.:.:0,8,17,25,35,45,55,67,79,91,105,120,137,155,176,199,226,257,296,346,417,537,1800 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:51,0:51:11:.:.:0,11,23,36,50,65,82,100,120,144,170,202,241,291,361,482,1800 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:36,0:36:7:.:.:0,7,14,22,30,38,47,57,67,78,89,102,116,132,149,169,192,219,252,294,354,456,1530 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:45,0:45:7:.:.:0,7,15,23,32,41,50,60,70,82,94,107,120,136,152,170,191,214,241,272,311,361,432,552,1800 0|1:0,3:3:25:0|1:53637_T_G:123,0,25:53637 ./.:0,0:0:.:.:.:0,0,0 ./.:0,0:0:.:.:.:0,0,0 ./.:0,0:0:.:.:.:0,0,0 ./.:0,0:0:.:.:.:0,0,0 ./.:0,0:0:.:.:.:0,0,0 ./.:0,0:0:.:.:.:0,0,0 ./.:0,0:0:.:.:.:0,0,0 0/0:1,0:1:3:.:.:0,3,22 0/0:1,0:1:3:.:.:0,3,36 0/0:7,0:7:18:.:.:0,18,270 0/0:2,0:2:6:.:.:0,6,75 0/0:2,0:2:6:.:.:0,6,77 0/0:1,0:1:3:.:.:0,3,40 0/0:5,0:5:15:.:.:0,15,205 0/0:3,0:3:9:.:.:0,9,112 ./.:0,0:0:.:.:.:0,0,0 0/0:5,0:5:15:.:.:0,15,213 ./.:0,0:0:.:.:.:0,0,0 0/0:4,0:4:12:.:.:0,12,124