1
$\begingroup$

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

Improve this question
$\endgroup$
5
  • $\begingroup$ Cross-posted on GitHub for some reason: github.com/cancerit/ascatNgs/issues/84 $\endgroup$
    – Ram RS
    Apr 22 '19 at 13:32
  • 1
    $\begingroup$ 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
  • 1
    $\begingroup$ 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
0
$\begingroup$

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

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.