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A point mutation was missed by Mutect2 when read length redueced from 150bp to 75bp
I have been analyzing the NGS data from clinical cancer samples for diagnosis.
The NGS data are paired end reads with 150bp each.
Most of the paired end reads were overlapped because the DNA extracted from FFPE samples are likely to be degraded into short pieces less than 200bp.
So, I am thinking about reducing the read to 75bp if there are no differences in mutation detection.
Two types of read length (150bp and 75bp) were tested with one sample which was techincally repeated 6 times.
The 75bp reads were generated by cutting the original reads in half in fastq files.
In the analysis, one mutation (SNP) was missed with 75bp reads all the time but detected with 150bp reads.
The depth of the mutation was about 300bp, and its VAF was about 50% (heterozygous SNP).
Why Mutect2 could not detect the mutation with 75bp-reads?