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  • Samtools mpileup: Discrepancies in indel coverage

    In .vcf files outputted by samtools the coverage of indels is represented by the IDV(Maximum number of reads supporting an indel) value. This value corresponds to what I see in IGV. But DP4 values for indels seem to be complete nonsense.

    The following insertion is supported by 3 reads, but DP4 says the alternate allele is covered by 199+199=398 reads. How can this be?

    16 68771414 16:68771414_T/TCCCCGCCCCAGCC T TCCCCGCCCCAGCC 222 . INDEL;IDV=3;IMF=0.00265957;DP=1127;VDB=0.816175;MQSB=0.998812;SGB=-0.693147;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=333,396,199,199;MQ=59

    Unfortunately I am unable to find any documentation how IDV values are calculated/filtered.

    Thanks,

    Christian

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