Closed fpbarthel closed 5 years ago
@anderkj2 compared GATK 4.1.0.0 Mutect2 (GATK in figure) variant calls versus GATK 4.0.x Mutect2 calls (freebayes in figure since later combined to a multisample vcf using freebayes to get allelic frequencies):
While there is a large overlap of about 20k variants, there is a huge number of GATK 4.0.x M2-only variants (22k). This could be explained by several factors:
Comparison of read depths between GATK 4.1 M2 and from Freebayes using the 20k variants that were analyzed in both demonstrates a lower depth from Mutect2 compared to Freebayes. Likely this can be explained by the more stringent read filters that apply in M2. The tail of indels that have a higher read depth in Mutect2 are all indels that Freebayes was not able to accurately count reads for.
Closing this issue, see also Slack discussion @fpbarthel and @anderkj2 .
Two open issues moved to new separate issues
To-do's related to SNV calls for the second data release
bcftools
, or M3 if already available. Throw away parallel calls across whole dataset and focus on parallel calls within a patient. Done using GATK 4.1 M2Collect coverage statistics per gene and sample.@fpbarthelAssess the impact of purity on sensitivity of M2 to detect variants, adjust mutational rates/counts by purity@fpbarthel