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cancerit / ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing
http://cancerit.github.io/ascatNgs/
GNU Affero General Public License v3.0
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hg38 Snp GC correction file #79

Closed Caninus23 closed 6 years ago

Caninus23 commented 6 years ago

Is there a possibility to generate such file for hg38?

keiranmraine commented 6 years ago

A script is included for this purpose. Documentation can be found in the wiki:

https://github.com/cancerit/ascatNgs/wiki/Convert-SnpPositions.tsv-to-SnpGcCorrections.tsv

keiranmraine commented 3 years ago

As a note for future use, the relevant file is included in this archive available from the Sanger FTP site:

ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/CNV_SV_ref_GRCh38_hla_decoy_ebv_brass6+.tar.gz

The file to extract is:

CNV_SV_ref_GRCh38_hla_decoy_ebv_brass6+/ascat/SnpGcCorrections.tsv
umasaxena commented 3 years ago

Hello, is this site update ? If you wouldnt mind could you please send me the current location for the "CNV_SV_ref_GRCh38_hla_decoy_ebv_brass6+/ascat/SnpGcCorrections.tsv" file.

keiranmraine commented 3 years ago

The location is unchanged. Most web-browsers no longer support ftp and you will need to use a dedicated client.

However, the file is also accessible via the http protocol (in web-browser):

http://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/CNV_SV_ref_GRCh38_hla_decoy_ebv_brass6+.tar.gz
umasaxena commented 3 years ago

Many thanks

KathyCat1 commented 1 year ago

How to get segment level of copy number like ASCAT for WES, with chr start- end per copy number
head ascat_out/J78AIS.copynumber.txt Chromosome Position Log R segmented LogR BAF segmented BAF Copy number Minor allele Raw copy number rs62635286 1 13116 -1.87555628113731 -0.0605505377127584 0 NA 3 1 0.343360059102869 rs62636497 1 15274 NA -0.0605505377127584 NA NA 3 1 NA rs806731 1 30923 0.692439784204986 -0.0605505377127584 0 NA 3 1 8.73542496544808 rs116400033 1 51479 -0.0667777124781612 -0.0605505377127584 1 NA 3 1 3.3553946036283 rs141149254 1 54490 -0.230861488577514 -0.0605505377127584 0 NA 3 1 2.72857614141887 rs28396308 1 55545 -0.0163521722183716 -0.0605505377127584 1 NA 3 1 3.57555015830608 rs114420996 1 58814 0.228953394000139 -0.0605505377127584 1 NA 3 1 4.87085609998217 rs62637817 1 60351 -0.570543243821012 -0.0605505377127584 0 NA 3 1 1.77835717443695 rs80011619 1 63671 0.316724969560093 -0.0605505377127584 1 NA 3 1 5.44057843492366

AndyMenzies commented 1 year ago

Hi

This project is a WGS specific wrapper around ASCAT. The underlying ASCAT algorithm has been updated to support WES data, although we don't.

Please see - https://github.com/VanLoo-lab/ascat

Andy