Conversion Of Pfb Files From Hg18 To Hg19

Question

[User 0559]

I am using pennCNV for copy number to generate genotype clusters, using data from Affy6.0. The function generateaffygeno_cluster.pl takes input affygw6.hg18.pfb (provided by pennCNV package) as reference. However, this pfb file is based on hg18, as indicated by its title.

How would I convert it into a file based on hg19? I found this discussion http://biostar.stackexchange.com/questions/1622/pfb-file-for-cnv-analysis-using-illumina-610-quad-v1-arrays on the forum. However, my problem is different from this one as I am trying to convert between different genome versions. Can anyone give a hint on how to do this? Can I use liftover to do this convertion? And how would that be done? Thank you very much!

[Ryan D]

You should not use the "code" tag for your questions.

[Neilfws]

For reference, indenting a line with 4 spaces results in code formatting.

Answer 1

[Ryan D]

Take your existing pfb and convert the file to something that can be read by LiftOver. Convert it to hg19. Convert back to pfb.

Convert your pfb like so:

awk '{print "chr"$2"\t"$3"\t"$3+1"\t"$1" "$4}' old.pfb > to_usc.txt

Upload the new text file to LiftOver available here: http://genome.ucsc.edu/cgi-bin/hgLiftOver.

Convert to hg19 and download your file back to your Linux machine. We'll say you saved the file as from_usc.txt.

sed 's/chr//g' from_usc.txt | awk '{print $4"\t"$1"\t"$2"\t"$5}' > new.pfb

So long as you don't have any markers with the letters "chr" in them and your sex chromomsomes, X and Y, aren't named as chr23/chr24, the LiftOver should be smooth. Check your file when you are done with:

cat new.pfb | cut -f1 | sort | uniq

Then you can make sure all chromosomes came across properly. Also, don't forget to check the "failure file" on the UCSC website to see if there were any LiftOver failures. Hope this helps.

Rx

[User 0559]

Thank you very much.. This is my first post and I am just starting high resolution genomics recently. Thank you for taking your time to answer this.

Answer 2

[Mark]

You should upload a file to the web for this, would be useful, so people don't have to go through these tedious steps in the future!

Best, Mark

[User 0559]

Thanks. This was my first post and I am not very sure about the details of my own question. Thank you for your remark. I will try to do what you suggested any time later on.

Thanks.