So what could possibly have introduced that 'N' into the sequence reads ?
Is it present in the original .fastq file ?
- tom blackwell -
On Tue, 4 Nov 2014, Arumilli, Meharji wrote:
> Hi,
>
> These are the commands used to call variants using samtools-0.1.19:
>
> samtools mpileup -ABugf ref.fa -l bed -d 1000000 bam | bcftools view -vcg - |
> vcfutils.pl varFilter -D 1000000 > out.vcf
> vcfutils.pl varFilter -Q 40 -d 10 out.vcf | awk '$6>=40' > fin.vcf
>
>
> Hope this might help to some extent.
>
>
> On 04/11/14 20:52, Thomas W. Blackwell wrote:
>>
>> 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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