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!
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User 0559 •
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
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.
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.
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