Question: vcf to vranges
0
gravatar for arsala521
3.3 years ago by
arsala52110
arsala52110 wrote:

Hello

I made vranges object from my VCF file usingreadVcfAsVRanges. There are 37974 variants in the VCF file and in vranges there are 14682016 ranges. Can someone please explain this difference?

I guess that if a variant is in more than one sample then there will be more than one range for that variant in vranges object but even then there are too many number of ranges.

Regards

 

 

 

ADD COMMENTlink modified 3.3 years ago by Valerie Obenchain6.7k • written 3.3 years ago by arsala52110
Answer: vcf to vranges
0
gravatar for Valerie Obenchain
3.3 years ago by
United States
Valerie Obenchain6.7k wrote:

The data are expanded (replicated into rows) by the number of ALT values as well as the samples which may explain the difference. Reading in a small subset with a 'param' would allow you to inspect manually to see what's going on, e.g.,

param <- ScanVcfParam(which=GRanges("chr6", IRanges(5000, 6000)))

readVcfAsVRanges(myfile, param=param)

Valerie

ADD COMMENTlink written 3.3 years ago by Valerie Obenchain6.7k

thank you so much.

 

ADD REPLYlink written 3.3 years ago by arsala52110
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