Running THetA2 with Varscan input?

Question

[hsbinf]

Hi,

I'm trying to get input file for THetA 2 using CreateExomeInput command. I'm giving the segment file for this command as the Varscan 2 output file after CBS segmentation with these columns

chr loc.start   loc.end num.mark        seg.mean

chr1    69268   12327976        1055    1.6745
chr1    12327999        12395859        112     1.33
chr1    12395959        12398149        3       -1.0807
chr1    12398177        12836275        167     1.3756

However, in the output I get 0 for both tumor count and normal count. I'm using hg19.fa & for the exon file I'm using hg19.exons.bed file as given in the THetA folder. Can someone please help if the output is 0 due to my input data or is there anything I can do to solve it.

Thanks

Answer 1

[j.p.albrecht]

Hi,

i had the same problem. After i used a different .bed file everything worked fine. (For obtaining a hg19.bed file see topic : Gff Or Bed File For Hg19 Genome)

Greetz

EDIT: Unfortunately it was not that easy. Here is the correct answer: Segment file, bed file,BAM files, and FASTA reference file have to be sorted karyotypically!!!

(I downloaded all hg19 chromosomes from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ and gunziped them in one file in the correct order from 1 to 22 and then X, Y)
Caution with chrM or chrUn in the middle -> producing wrong interval count file. put them if necessary at the end of your hg19.fa

Greetz