What'S The Meaning Of Variant Filtering Parameter 'Read Position'?

Question

[lyz10302012]

Can anyone tell me what is the meaning of the SNP filtering parameter 'Read Position' in some papers? I found the explaination 'Average variant position in supporting reads relative to read length ' in VarScan2's paper, but i still don't understand. Can anyone show me how to calculate it? Thanks.

Answer 1

[Sean Davis]

The read position is the position in the read at which the variant base was found. For Illumina sequencing, there tends to be lower quality bases at the 3' end of reads. If a variant is called using only those positions near the end of the read, it may be a less reliable call. The reported "read position" tries to capture such biases if present.