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Hi all. I'm a student working to identify tumor-specific mutations.
Recently I've came up to VarScan and SomaticSniper.
There are some confusions about using VarScan, and I see that the documentation is somewhat lacking in catching up its own versions, so I ask this question here
!
I'm using VarScan.v2.2.8.jar somatic when doing my analyses.
1. When What is the "germline p-value" exactly?
1.1. I see that --somatic-p-value sets a p-value to statistically test (Fisher's exact test) whether "normal variant allele frequency of one locus" is the same as "tumor variant allele frequency of one locus".
( Many thanks about the discussion here (it really was a great help!
):
http://seqanswers.com/forums/showthr...hlight=varscan )
So for example, I thought such contingency table could be made (I drew it crudely because I could not put in spaces instead of hyphens and underscores; ugly, isn't it?):
------------Normal--Tumor
Reference___10______2
1 Variant_____2______8 --> Fisher's exact p-value calculated.
...where the counts are reads mapped to the locus.
1.2. However, how can a "germline p-value" be calculated? D. Koboldt (the developer) himself explained that this germline p-value is "the null hypothesis is that the sample is homozygous-reference; under this hypothesis, all reads should support the reference base", which I do not understand exactly. I ask for a comment about this matter.
2. Can VarScan emit output in VCF (variant call format)?
It is written that now VarScan supports output to be in VCF, as written on the main web page as "VarScan v2.2.8 released with new somatic calling features: Tumor-normal mpileup compatibility and VCF 4.1 output option." (http://varscan.sourceforge.net/index.html)
However, all I can find inside the documentation (or I'm doing something wrong) is about v2.2, not v2.2.8.
I really hope somebody could give me a warm hand.
Have a great day!!
Recently I've came up to VarScan and SomaticSniper.
There are some confusions about using VarScan, and I see that the documentation is somewhat lacking in catching up its own versions, so I ask this question here
!I'm using VarScan.v2.2.8.jar somatic when doing my analyses.
1. When What is the "germline p-value" exactly?
1.1. I see that --somatic-p-value sets a p-value to statistically test (Fisher's exact test) whether "normal variant allele frequency of one locus" is the same as "tumor variant allele frequency of one locus".
( Many thanks about the discussion here (it really was a great help!
):http://seqanswers.com/forums/showthr...hlight=varscan )
So for example, I thought such contingency table could be made (I drew it crudely because I could not put in spaces instead of hyphens and underscores; ugly, isn't it?):
------------Normal--Tumor
Reference___10______2
1 Variant_____2______8 --> Fisher's exact p-value calculated.
...where the counts are reads mapped to the locus.
1.2. However, how can a "germline p-value" be calculated? D. Koboldt (the developer) himself explained that this germline p-value is "the null hypothesis is that the sample is homozygous-reference; under this hypothesis, all reads should support the reference base", which I do not understand exactly. I ask for a comment about this matter.
2. Can VarScan emit output in VCF (variant call format)?
It is written that now VarScan supports output to be in VCF, as written on the main web page as "VarScan v2.2.8 released with new somatic calling features: Tumor-normal mpileup compatibility and VCF 4.1 output option." (http://varscan.sourceforge.net/index.html)
However, all I can find inside the documentation (or I'm doing something wrong) is about v2.2, not v2.2.8.
I really hope somebody could give me a warm hand.
Have a great day!!
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