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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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Problem generating SNPpositions for GRCh38 #92

Open WillieYu opened 4 years ago

WillieYu commented 4 years ago

There appears to be no "E_Multiple_observations" entries for GRCh38 1000genomes phase3 vcfs. I checked phase3 vcfs for release91 and release99 from ENSEMBL. Is there an alternative method to generate the SNP positions for GRCh38 since I want to use ascatNGS for GRCh38 aligned bams.

keiranmraine commented 4 years ago

The data is available on our FTP site:

ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/

Specifically this file CNV_SV_ref_GRCh38_hla_decoy_ebv_brass6+.tar.gz.

$ ftp ftp.sanger.ac.uk
Connected to ftp-sanger-ext.sanger.ac.uk.
220 ProFTPD 1.3.5a Server (WTSI Public FTP Server) [::ffff:193.62.203.115]
Name (ftp.sanger.ac.uk:XXX): anonymous
331 Anonymous login ok, send your complete email address as your password
Password: XXX
230 Anonymous access granted, restrictions apply
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> ls pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/
200 PORT command successful
150 Opening ASCII mode data connection for file list
drwxrwxr-x   2 ftp      ftp          4096 May  3  2019 201904
drwxrwxr-x   2 ftp      ftp          4096 May  3  2019 201905
drwxrwxr-x   2 ftp      ftp          4096 Oct 15  2019 201906
lrwxrwxrwx   1 ftp      ftp            42 Jun 11  2019 bwa_idx_GRCh38_hla_decoy_ebv.tar.gz -> 201906/bwa_idx_GRCh38_hla_decoy_ebv.tar.gz
lrwxrwxrwx   1 ftp      ftp            53 Jun 11  2019 CNV_SV_ref_GRCh38_hla_decoy_ebv_brass6+.tar.gz -> 201906/CNV_SV_ref_GRCh38_hla_decoy_ebv_brass6+.tar.gz
lrwxrwxrwx   1 ftp      ftp            43 Jun 11  2019 core_ref_GRCh38_hla_decoy_ebv.tar.gz -> 201906/core_ref_GRCh38_hla_decoy_ebv.tar.gz
lrwxrwxrwx   1 ftp      ftp            17 Oct 15  2019 GRCh38.md5 -> 201906/GRCh38.md5
lrwxrwxrwx   1 ftp      ftp            45 Jun 11  2019 qcGenotype_GRCh38_hla_decoy_ebv.tar.gz -> 201906/qcGenotype_GRCh38_hla_decoy_ebv.tar.gz
-rw-rw-r--   1 ftp      ftp           877 Jun 11  2019 README.md
lrwxrwxrwx   1 ftp      ftp            57 Jun 11  2019 SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment.tar.gz -> 201906/SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment.tar.gz
lrwxrwxrwx   1 ftp      ftp            57 Jun 11  2019 VAGrENT_ref_GRCh38_hla_decoy_ebv_ensembl_91.tar.gz -> 201906/VAGrENT_ref_GRCh38_hla_decoy_ebv_ensembl_91.tar.gz
226 Transfer complete

We need to document this

WillieYu commented 4 years ago

Thanks for the prompt response. I am downloading the file you indicated right now.