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
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