Hi,
First, I wish you all a 2022 of health and success:)
Second, I am trying to understand the output from the mpileup tool but I
am unsure what the "<*>" is in the ALT column is. It appears in every line
and sometimes in conjunction to another base. I realize that some people
have the same doubt, however I could not find a clarifying answer.
Is this related to INDELS? I notice I cannot find any INDELS. However, the
strange thing is that "<*>" appears with a depth of 0
Could you please
help?
I am using the following command:
bcftools mpileup -f ref_genome/ref.fasta results/bam/sorted.bam --annotate
AD > sample.mpileup
As an example I am copying one output line below:
NC_045512.2 102 . G A,<*> 0 .
DP=285;I16=194,32,1,0,9491,424267,36,1296,13560,813600,60,3600,3928,78818,6,36;QS=0.996221,0.00377873,0;SGB=-0.379885;RPBZ=-1.54189;MQBZ=0;MQSBZ=0;BQBZ=-0.532247;SCBZ=-0.133926;FS=0;MQ0F=0
PL:AD 0,255,255,255,255,255:226,1,0
Thank you so much,
Bárbara
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