Q1:
The psiDR is a valuable resource for my research.

In the corresponding publication (The GENCODE pseudogene resource, Pei et
al., Genome Biology, 2012), you describe in "Material & Methods:
Identification of the parents of pseudogenes and sequence similarity to
the parent" that the exons of parent and pseudogenes were used to align
them via ClustalW2.

Is it possible to provide me the alignments? That would be great.

A1:
Edit @PATH

Q2:
That is, can we run VAT (snpMapper) on a simple mutation list (as shown below)?
##fileformat=VCFv4.0
#CHROM POS ID REF ALT QUAL FILTER INFO
14 30525048 . . . . . .
19 28364092 . . . . . .
2 144165461 . . . . . .
2 144224307 . . . . . .
4 98318053 . . . . . .

No rs numbers, no sample IDs and no group:sample files are present in this case, as I just wanted to run VAT for a list of somatic mutations to see if they are annotated to a coding or non-coding region.

There will be no duplicates in the list too, as I have already handled their frequency beforehand.

A2:
I will update documentation on VAT. Thanks for pointing it out to us. Regarding the input that is a non-vcf file,
just make a dummy vcf file. That is have extra columns that are tab-delimited.. Please e-mail me if you have more questions. However, bear with me as my computer just died and I am trying to get it fixed.