The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Can a SNP with 35 vs 54 reads really be homozygous?
We have sequencing information for a whole family (father, mother, 3 kids) and analyzed them with the gatk (more info below). And while looking through the results I found a SNP with these predicted genotypes and read frequencies:
kid 1: 0/0, 168 vs. 26 reads
mother: 0/0, 211 vs. 34 reads
father: 0/0, 220 vs 18 reads
kid 2: 1/1, 35 vs. 54 reads
kid 3: 1/1, 20 vs. 42 reads
First it caught my eye because of the impossible heredity but than I also noticed the, at least to me, strange genotype calls for kid 2 and 3. Can you explain the effects that lead to such results?
exact vcf entry:
4 71347185 . T C 332.95 . AC=4;AF=0.400;AN=10;BaseQRankSum=3.959;DP=828;Dels=0.00;FS=0.000;HaplotypeScore=11.5830;MLEAC=4;MLEAF=0.400;MQ=29.13;MQ0=153;MQRankSum=-6.418;QD=2.20;ReadPosRankSum=-10.775;SOR=0.708 GT:AD:DP:GQ:PL 0/0:168,26:194:99:0,157,2194 0/0:211,34:245:93:0,93,2661 0/0:220,18:238:99:0,101,2422 1/1:35,54:89:15:131,15,0 1/1:20,42:62:27:250,27,0
pipeline (not all under my control):
- mapper is unknown, probably bwa
- Picard MarkDuplicates (Version 1.128)
- GATK IndelRealigner (Version unknown)
- GATK UnifiedGenotyper (Version 3.4-46), I know it is deprecated but we had to use it for a reason