I have run variant calling using samtools with the following settings:
samtools view -bq 20 -F 1796 bamfile.bam | samtools mpileup -EDSgu -d 5000 -f
Refseq.fa -L 5000 -F 0.05 -| bcftools view -Nvg - > Variants.vcf
I generated a list of variants however I am confused why no variant was called
for the site below:
#CHROM POS ID REF ALT QUAL FILTER INFO
FORMAT
chr11 8693405 . G . 23.8 .
DP=106;VDB=4.848171e-01;AF1=1;AC1=2;DP4=0,0,28,77;MQ=60;FQ=-35.6
PL:DP:SP 255:105:0
When I look at the calls made using mpileup I can see that all sites are either
A or T (see below) (read depth 105) so it seems completely incorrect to call
the Ref base which is G.
mpileup
chr11 8693405 G 105
taTAattAttATaatatTttATTtaaaTtaaAtATaAtttTttttTatAaTTaaatttaaTTtattAAtaatTtttattAaaatatttatAaataTataattaaA
?=@@=@@?>=?A>>=>@A>@@?A@@>@A@@>A>AA??>>>?@A@@@?@A??A@@??A?>?AAA?>>?A@AA??A?AA@A>A?A?AAAA?>@?????>@?A@A>??
This data is taken from high read depth sequencing of the HapMap sample NA12878
so I know that at this position the correct call should be:
chr11 8693405 . G A,T 24600 PASS
BasesToClosestVariant=668;LEN=1,1;TYPE=snp,snp GT 2|1
So the correct bases seem to be aligning just that the variant is not being
called.
I am using samtools version 0.1.19
Any suggestions what might be happening here.
Many thanks
Kevin
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