As with the earlier question, we are all puzzling what could possibly
have introduced N's into the sequence reads. No details of upstream
processing steps are given, so no one has any ideas to contribute.
Simplified command lines and software version numbers are always helpful.
- tom blackwell -
On Tue, 4 Nov 2014, Arumilli, Meharji wrote:
> 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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