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GATK 4.1 HaplotypeCaller detected the same variant in one technical replicate, but failed in another
I tried to use GATK 4.1 HaplotypeCaller to detect EGFR T790M variant in a few technical replicates. It turned out that HaplotypeCaller detected the same variant in one technical replicate, but failed in another replicate. The sample is the commercial EGFR T790M positive control.
The following are the IGV screenshots, the first one HC called T790M while the bottom one HC failed even though we can see T790M in both pre-processed and HC bamout bam files.
I also have a few diluted sample runs with no T790M detection and the bamout bam files have no read at all at that region while the reads are there in the pre-processed bam files.
These are amplicon based data with very high depth ( > 12,000x). I tried to adjust parameters and so far --max-reads-per-alignment-start 0 --disable-read-filter NotDuplicateReadFilter --adaptive-pruning true --kmer-size 10 --kmer-size 15 --kmer-size 20 --kmer-size 25 --kmer-size 30 is the best I can get as I can identify T790M from 4 out of 12 T790M positives.
Thanks a lot for the help!