hg18 to GRCh38 through chain files

[Alexandra Vatsiou]

Hello,

I know that the chain file is sufficient to convert from one assembly to another the SNP coordinates. 

I have the following questions:

1. I suppose the reference sequence is the hg18 and the query is the hg38 in the hg19ToHg38.over.chain file. Right?

  

2. However, I can't see how exactly I will do the conversion of SNP coordinates between the two assemblies. The chain file contains 

a) the size of the ungapped alignment and

b) the difference between the end of this block and the beginning of the next block in the reference and the query sequence. 

What I have is something like the following:

SNP              chr      genetic dist     physical dist

rs12565286 1 0.000881697 711153 C G

rs11804171 1 0.0058782819 713682 A T

rs2977670 1 0.0060252705 713754 C G

rs2977656 1 0.018904623 719811 C T

rs12138618 1 0.0633989027 740098 A G

where the fourth column is the SNP coordinates of each SNP.

For example according to the chain file what will be the coordinate of the first SNP?

I will greatly appreciate if anyone knows how to deal with this.

Look forward to your reply.

Regards,

Alexandra

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Alexandra Vatsiou