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Running THetA2 with Varscan input?
Entering edit mode
13 months ago
hsbinf • 20


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.


Entering edit mode
2.8 years ago
j.p.albrecht • 30


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)


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 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



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