In a project of mine, I used funcotator to annotate somatic mutations using the following command:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /wynton/home/cbi/shared/software/CBI/gatk-22.214.171.124/gatk-package-126.96.36.199-local.jar funcotator --data-sources-path /wd/funcotator_dataSources.v1.7.20200521s -R /wd/ucsc.hg19_M_1_22_X_Y.fasta --ref-version hg19 -V /wd/SC300025_new.vcf -O SC300025.maf --output-file-format MAF.
However, the annotation result does not exactly match the ANNOVAR annotation. Therefore we checked a few different annotations in IGV and found that the funcotator gave the incorrect protein change.
For example, this is one of the PKD1 mutation I identified with funcotator:
But in fact the protein change should be: p.L2169S.
Could you please help me figure out the root cause for this and how to remedy this? This issue is troubling me because not all the annotations are off (most are correct) so it is difficult to systematically identify the incorrect ones.
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