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Hi,
Using Samtools I have obtained a .vcf file with some variants, including INDELs. I am trying to compare them to 1000g for frequency, but I am finding difficulties trying to find the INDELs according to position.
For example, Samtools detected the following deletion
chr7 107052927 AACA AA
when transforming this deletion to Annovar format, I get the following coordinates and nomenclature:
chr7 107052929 107052930 CA -
And I have manually found this deletion in the latest 1000g database as
chr7 107052928 107052928 AC -
So it is difficult to define a method to annotate this deletion that would be automatic for any INDEL, isn't it?
Has anyone found a similar situation? how would people annotate INDELs using 1000g database?
Apart from that, would you say that 1000g nomenclature is not appropriate for this deletion?
Cheers,
Dave
Using Samtools I have obtained a .vcf file with some variants, including INDELs. I am trying to compare them to 1000g for frequency, but I am finding difficulties trying to find the INDELs according to position.
For example, Samtools detected the following deletion
chr7 107052927 AACA AA
when transforming this deletion to Annovar format, I get the following coordinates and nomenclature:
chr7 107052929 107052930 CA -
And I have manually found this deletion in the latest 1000g database as
chr7 107052928 107052928 AC -
So it is difficult to define a method to annotate this deletion that would be automatic for any INDEL, isn't it?
Has anyone found a similar situation? how would people annotate INDELs using 1000g database?
Apart from that, would you say that 1000g nomenclature is not appropriate for this deletion?
Cheers,
Dave