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samtools/bcftools 0.1.19 IS field (indel fraction)



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  • samtools/bcftools 0.1.19 IS field (indel fraction)

    Dear all,

    I have been looking in vain for documentation on how the "fraction of indel reads" is calculated that appears in the INFO field IS in the vcf output after samtools/bcftools (version 0.1.19).
    It seems that this number is not based on the "maximum number of reads supporting the indel" divided by any of the depth values (DP, DP4, sample_DP).
    Does anyone know how this fraction value is calculated?

    Also, do you know, how the "maximum" number of reads is determined? Is it the highest number of indel reads found in any one sample in the analysis?

    This is all it says in the vcf header about the IS field:
    ##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">

    Any comment or explication is highly appreciated.

    Many thanks,

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