questions about input for scarHRD

[Huan-Wang-S4]

Hi,

I'm reading the input example files from here (https://github.com/sztup/scarHRD )

##   chromosome position base.ref depth.normal depth.tumor depth.ratio    Af
## 1       chr1    12975        N            7          20       2.841 1.000
## 2       chr1    13020        A            8          28       3.500 0.964
## 3       chr1    13026        N           15          43       2.964 1.000
## 4       chr1    13038        T           11          35       3.182 0.971
## 5       chr1    13041        A           11          37       3.364 0.946
## 6       chr1    13077        N           26          65       2.465 1.000
##   Bf zygosity.normal GC.percent good.reads AB.normal AB.tumor tumor.strand
## 1  0             hom         60         51         N        .            0
## 2  0             hom         60         28         A   G0.036         G1.0
## 3  0             hom         59         51         N        .            0
## 4  0             hom         59         35         T   C0.029         C1.0
## 5  0             hom         59         37         A   G0.054         G0.5
## 6  0             hom         62         51         N        .            0

I wonder if you could explain a bit more for some of the columns?

• depth.ratio doesn't appear to be identical as depth.tumor / depth.normal
• I assume Af is ref allele frequency in the tumor sample, but what does Bf mean? Af + Bf don't always add up to 1. Isn't that weird?
• GC.percent. How do you have GC.percent for a single nucleotide position?
• good.reads. What's the meaning?
• tumor.strand. What this means?
• Why for some positions we have N for base.ref?

Thanks

Huan

[tanasa]

Hi Huan. I have a similar question to yours. Namely how can I transform the traditional type of input into scarHD (A) (generated by sequenza):

chromosome position base.ref depth.normal depth.tumor depth.ratio Af
Bf zygosity.normal GC.percent good.reads AB.normal AB.tumor tumor.strand

into the abbreviated version of the input data (B) :

SampleID Chromosome Start_position End_position total_cn A_cn B_cn ploidy

What transformation shall I use to convert A into B ? Thanks so much,

Bogdan