Q1:
We are very interested in your AlleleSeq package. I have downloaded the maternal.chain and paternal.chain from http://sv.gersteinlab.org/NA12878_diploid/NA12878_diploid_dec16.2012.zip<http://sv.gersteinlab.org/NA12878_diploid/NA12878_diploid_dec16.2012.zip.

From the documentation @http://info.gersteinlab.org/AlleleSeq:
Chain files
Using the chain file, one can use the LifeOver tool to convert the annotation coordinates from reference genome to personal haplotypes.

However, when I tried to liftOver my bed file using maternal.chain, all returned unMapped.

[liuh@helix NA12878_diploid_genome_dec16_2013]$ more maternal.chain
chain 249198044 1 249250621 + 0 249250621 1_maternal 249242013 + 0 249242013 1
10329 1 0
109 1 0
30199 3 0
43187 4 0
40 1 0
…

My bed file:
[liuh@helix bcf3]$ awk ‘{print $1,$2,$3}’ cyto.vcf.bed |head
chr1 14541 14542
chr1 14652 14653
chr1 14676 14677
chr1 14906 14907
chr1 14929 14930
chr1 15014 15015
chr1 16287 16288
chr1 16297 16298
chr1 16377 16378
chr1 16494 16495
…
My script:
module load ucsc; liftOver cyto.vcf.bed maternal.chain cyto.liftover unMapped.cyto

I tried to liftOver my bed from hg19 to hg18 without any problem. It means
that the bed file format should not have any issue.

A1:
thanks for interest to our software.
I may be wrong but it looks to me that the liftOver failed because of using different chromosome naming convention in .bed and .chain files.
In .bed file chromosomes are named with prefix ‘chr’, while in chain files they don’t have such prefix.

Q2:
Thanks so much for your time and kind help! It works well after I removed prefix ‘chr’ in bed file.

Do you have chain file(s) which can convert the annotation coordinates from maternal or paternal genome to reference genome?

I have mpileup and VarScan outputs with the annotation coordinates from maternal and paternal genome, and want to annotate it using annovar (but the annotation coordinates from the reference is required).

A2:
Incidentally, a previous user of AlleleSeq looking for conversion of mat/pat
to ref genome has given us an R code for public consumption. The only gripe
is we have not had time to test it extensively, hence we did not provide it
on the website previously.

I have the link here: http://alleleseq.gersteinlab.org/tools.html. The R
script converts mat/pat back to ref genome using the chain files provided by
AlleleSeq. Please see if it suits your purpose.