Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!

Relationship between depth and genotype?

AnneBAnneB UIC ChicagoMember

Hi, I am new to WGS and would like to know how the genotype is attributed. It seems it does not depend much on depth of allele ratio. We ran GATK3.6 and Freebayes on the same BAM 50-50X files and intersected them to reduce the number of variants between monozygotic twins (300k per caller). We got 16k residual variants after intersect that we need to filter and prioritize. GATK has much better concordance of allele ratio with genotype than Freebayes which gives much higher coverage. (1) What is the relationship between coverage (individual allele depth) and genotype? (2) Should we trust more allele balance or depth upon filtering? (2) What is the best practice to filter out variants from WGS? Thank you -Anne



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Hi there,

    In a nutshell, the QUAL score of the variant call (across one or more samples) is directly influenced by the amount of coverage at that site. However, the genotype assignment to a particular sample depends more on how well the available reads support one or more haplotypes. This is documented in some detail in the Methods docs as well as the workshop presentations (see blog for recent slidedeck link).
Sign In or Register to comment.