SNPs with missing INFO tags from bcftools mpileup

Question

[malonzm1]

Hi,

I used bcftools mpileup. My question is, why are there SNPs with missing INFO tags, e.g. VDB, RPB, MQB, BQB, MQSB?

chr1    10540   .       A       <*>     0       .       DP=1;I16=0,1,0,0,36,1296,0,0,0,0,0,0,0,0,0,0;QS=1,0;MQ0F=1      PL         0,3,4

Thanks for any help.

Answer 1

[iraun]

As you can see, the alternative allele is missing, therefore, those fields which are related with the alternative allele cannot be computed.