kchen-lab / texomer Goto Github PK

Hi,
I read in the "Examples" part "The bam file should be aligned based on GRCH38. ". It stands true for all analyses or just for the example you put? So, can I use also GRCH37 (if I aligned both RNA-seq and WES data on GRCH37)?
Also, I saw that in the sequenza.R script, hg19 is used as assembly. So, is there an error somewhere?
Kind regards,
Serena

Can I use the output of mutect instead of varscan？

Dear Professor Chen,

In investigating the application of this software to the WES dataset, I found that some somatic mutations derived from Varscan2 (using the Varscan2 default command: java -jar VarScan.v2.3.9.jar somatic XXX.mpileup YYY.mpileup) seem not somatic actually. Would such a phenomenon affect the optimization of purity estimate because this step takes the somatic mutations into consideration? And, more importantly, would it affect the quantification of intratumor heterogeneity (this procedure compares the distribution of somatic mutation and the germline mutation distribution)? If the somatic mutations are wrongly adopted, the final results of heterogeneity evaluation might be biased.

I am looking forward to hearing from you.

Best wishes,

Why does the documentation only refer to WES? Wouldn't it work equally well with WGS, just much slower?

The latest release has a genome doubling analysis feature but none of the documentation explains which output file the whole genome duplication status is in. Also, is there any estimate of if SNVs happen before genome doubling or after it?

I get following error and it looks like it happens when the code can not find the right SNV element for a given chromosome

Traceback (most recent call last):
File "/lab/Software/Texomer/Texomer.py", line 369, in
main()
File "/lab/Software/Texomer/Texomer.py", line 350, in main
SNVexp(germline=germlinename,somatic=somaticname,samfile=samfilename,outputname=outputname,case=case,bedtools=bedtools)
File "/lab/Software/Texomer/Texomer.py", line 132, in SNVexp
temppos=sorted(list(set(SNPpos[str(chromosome)])))
KeyError: 'chrY'