Hi,
I have attached two screenshots from samtools tview. One of them is
normal where the variant is not called with reference sequence on the
top and other with variant called as "AN". Does this help to infer further?
On 04/11/14 21:26, Thomas W. Blackwell wrote:
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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