We have a known SNV with AF ~1% and are trying to use Mutect2 to detect it in amplicon sequencing data.
- It can be called with GATK 126.96.36.199 without problems in multiple samples.
- It cannot be called in GATK 188.8.131.52 and GATK 184.108.40.206 with the same bam files input for multiple samples.
- When running in debug mode, the log revealed that the region is not assembled successfully in GATK 4.2 (Error: Not using kmer size of 10 in read threading assembler because it contains a cycle) and thus the variant is not called.
- In many cases, they have the same input reads and even same active region. But GATK 4.2 cannot assemble it while GATK 220.127.116.11 has no problem assembling the region.
We would like to understand if there is any assembler changes introduced in GATK 4.2+, which may cause the discrepancy between v18.104.22.168 and v4.2+? And is there any parameter we could set up to recover the expected SNV with GATK 4.2+? Any suggestions will be very much appreciated.
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