[bobo xin]

somatic-p-value

I'm new for Vanscan,I have some questions about somatic-p-value. when I call somatic variation ,I set somatic-p-value 0.05 , but in my results varscan has defined as somatic several positions with a p larger than 0.05,anybody can tell me why??

[m_two]

See above response from jjinking on 11-08-2012.
"If the alternate allele frequency among the reads is 0.0 for the normal sample and the tumor sample genotype is heterozygous, then VarScan will ignore the somatic p-value threshold and classify the variant as "Somatic"."

[bobo xin]

See above response from jjinking on 11-08-2012.
"If the alternate allele frequency among the reads is 0.0 for the normal sample and the tumor sample genotype is heterozygous, then VarScan will ignore the somatic p-value threshold and classify the variant as "Somatic"."

Thank you ,I misssed it

[Jane M]

Hello,

I used VarScan2 in the somatic mode for WES of paired samples. Now, I have WGS data of paired samples. It seems to me that in theory, there is no reason for not using VarScan2 in the same way on WGS data. In my search of how to process these data, I haven't seen someone using VarScan. Is it because of time consumption (With SomaticSniper, it takes around 5 hours for genome samples of 27 and 28x - with varScan2, it takes around 3 hours for exome samples with 100-100x)? Or is there additional reason?

Jane

[LIFS]

Dear Jane,

Any idea why I got this error message when running VarScan compare
File 1: ./Control_RF.vcf
File 2: ./Tumor_RF.vcf
Loading positions from file 1
Warning: Unable to parse chrom/position from #CHROM POS ID
REF ALT QUAL FILTER INFO FORMAT Blood

Thanks,
LIFS

[atpoint]

I had the same error message using processSomatic. It turned out to be a problem with the locate, which was non-UTF-8, see here on Biostars. Add

export LC_ALL=en_US.UTF-8

to the beginning of your script and retry.