Hi,
I have performed variant calling with samtools. For, some reason some of the
variants have N in ALT column as shown below:
Chromosome Position SNPid Reference Alternate QUAL
MQ DP
chr21 29989187 . A AN 96.50 60 46
This is a homozygous mutation supported by 46 reads with MQ of 60.
Checked the bam file for this position using mpileup
samtools mpileup -AB -f ref.fa -r chr21:29989186-29989188 input.bam
The output is
chr21 29989187 A 49 ....,,,,..,,,,+1n,,...,,,,..,,,,,...,,,...,..,,.,.,^].
7BF<<FFFB7FF<0FIFIIIFBFIIBFFF<IIIFFB<IIFII7BIBIBB
Is this a bug in the code that it is called as "AN" insertion. How
should i infer this mutation.
Any comments from the users of this community are highly valuable.
Br
Mehar
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