Dear Sir or Madam,
I am writing to report a problem of DP4 calculation for InDel by using
samtools-1.2. Following example shows a deletion.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT call_mv.vcf
refid 3349 . cccccccg c 162 . INDEL;IDV=193
;IMF=0.00417803;DP=46112;VDB=1;SGB=-0.693147;MQSB=0;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;
DP4=5412,12653,4220,3053;MQ=59 GT:PL:DP:DV:SP:DP4:DPR
0/1:195,0,255:25338:7273:.:5412,12653,4220,3053:18065,7255
The value of IDV (Maximum number of reads supporting an indel) is 193
According to DP4 (Number of high-quality ref-forward , ref-reverse,
alt-forward and alt-reverse bases), the number of alt bases is
4220+3053=7273
Could you tell me how does samtools calculate high-quality alt bases in
deletions? In the above example, the deletion is 7 bp in length. 7 * 193
(IDV) = 1141 < 7273 (sum of alt bases in DP4). How do explain DP4 in
Deletion? Thank you.
Sincerely,
Yitao
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