How to filter the germline INDELS?
I have done basic filtering of INDELS which are mentioned in GATK best practice? Still I have lots of indel. I have increased sample depth to 50, variant allele frequency to 0.5. Further I have calculated indel length. I found some indels are higher in length. More than 150 base pairs. Is it fine to keep indel length ≤ 10 to get less number of false positives?
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