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Long time I am struggling how to provide GISTIC2 required input like Num_Probes and Segment_Mean

I have called somatic copy number by scatngs and I have copy number output file (attached);

https://www.dropbox.com/s/r6nef2v1j2di6q6/my.copynumber.caveman.csv?dl=0

This is few lines of scatngs copy number output

1,1,13116,665401,2,1,3,1
2,1,668374,96324627,2,1,2,1
3,1,96326095,96419709,2,1,1,0

In scatngs reference paper says in this file we have

Segment number

Chromosome

Start position (origin-1)

End position (origin-1)

Major copy number—normal

Minor copy number—normal

Major copy number—tumor

Minor copy number—tumor

scatngs also returns another output like below

https://www.dropbox.com/s/7i28vooixdp06c2/WTSI-OESO_121_1pre.copynumber.txt?dl=0

Chromosome  Position    Log R   segmented LogR  BAF segmented BAF   Copy number Minor allele    Raw copy number
rs62635286  1   13116   -0.0290741822638953 0.245246748556562   0.25    NA  3   1   2.35806652809599
rs75454623  1   14930   0.402869048014209   0.245246748556562   0.3095  NA  3   1   4.14031506947036

I am wondering how I can get Num_Probes and Segment_Mean From this files?

People say

Segment_Mean = log2(tumour copy number / 2)

So, does that mean I should add up Major copy number—tumor and

Minor copy number—tumor to get tumour copy number? for getting Num_Probes what should I do?

EDITED

people says

scatngs uses read counts at SNPs to generate calls and so the locations of the SNPs is what I need to generate the number of markers in each segment. (eg each SNP = 1 marker).

Do they mean, for instance if the position of SNP rs62635286 is 13116, so the num_prob is 13116?

Any help please?

Thanks a lot in advance

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  • $\begingroup$ Cross-posted on GitHub for some reason: github.com/cancerit/ascatNgs/issues/84 $\endgroup$
    – Ram RS
    Apr 22 '19 at 13:32
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    $\begingroup$ I mentioned a cross-post. That does not stop anyone from reading the question or helping you. $\endgroup$
    – Ram RS
    Apr 22 '19 at 13:52
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    $\begingroup$ Mentioning a cross post is hardly negative feedback or reason to ignore a post that belongs on bioinfo SE. $\endgroup$
    – Ram RS
    Apr 22 '19 at 14:16
  • $\begingroup$ Did you try reading the GISTIC2 documentation about how to get the data in that format? Or perhaps they point to a known file extension (or a weird one from only a single program) I tried searching on a couple of website about these required Num_probes but couldn't find anything. Are you using this software or other with the same name? $\endgroup$
    – llrs
    Apr 23 '19 at 10:32
  • $\begingroup$ I read GISTIC2 documentation, there is nothing about how to get required format. Exactly I am trying the same software you are referring to. People using GISTIC in broad institute produce their CN by this method that returns format for GISTIC software.broadinstitute.org/gatk/documentation/… $\endgroup$
    – Exhausted
    Apr 23 '19 at 10:36
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Depends on the software to generate the segmentation file;

For example I have used scatngs for segmentation that for sample returns

Segment number
Chromosome
Start position (origin-1)
End position (origin-1)
Major copy number—normal
Minor copy number—normal
Major copy number—tumor
Minor copy number—tumor

By log2(Major copy number—tumor + Minor copy number—tumor /ploidy of each sample) you would get segment mean

For number of probes

The number of probes depends on where the data came from.
1) From SNP arrays:  Number of array probes within each segment.
2) From exon capture data:   Probes are the ends of exons and so the number of probes are equal to the number of exons  X 2.
3) From whole genome sequencing:  Probes are the boundaries of bins used to generate the copy number data and so the number of probes are equal to the number of bins + 

For example in my case for scatngs

Each SNP is a marker, and so you have to count how many of these SNPs are on each segment

I have asked this question in

Extracting the number SNP in each range

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