a question about SNP version file

[dina volodarsky]

Hello,

I need a SNP annotation file for a mapping project which was sequenced with 454.

Which file should I use? 141 or 142? I tried the 142 but the mapper software(454) produces an error with it.

thank you for your help,

Dina

[Matthew Speir]

Hi Dina,

Thank you for your question about SNP data here at UCSC. What's the name
of the SNP file you downloaded, and where did you download it from? What
program are using to analyze your sequencing data and annotate SNPs?
What errors messages did you see when running this program with the file
SNP 142 you previously downloaded?

I hope this is helpful. If you have any further questions, please reply
to genome...@soe.ucsc.edu. All messages sent to that address are
archived on a publicly-accessible Google Groups forum. If your question
includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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>

[Matthew Speir]

Hi Dina,

Thank you for providing more information about what you are trying to do. Many of the files on our download server, like http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/snp142.txt.gz, contain an extra "bin" column that speeds up their display in the Genome Browser. This bin column may be interfering with your ability to run the mapping software using that file. You can use the following command to remove this bin column:

    cut -f 2- snp142.txt > snp142.noBin.txt

You may also want to contact 454 about this issue as well, as they could have other ideas about what may be causing the issue.

I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

On 10/6/15 11:59 PM, dina volodarsky wrote:

While mapping first there are warnings: unknown line format in snp annotation file,,, for many lines,

then: Warning: snp annotation contains many lines with unknown formatting

and then

unable to parse known snp file..

On Wed, Oct 7, 2015 at 9:34 AM, dina volodarsky <di...@dyn.co.il> wrote:

Hi

Thank you for your reply. I downloaded SNP142.txt and SNP 141.txt from the annotation part in ucsc. i use the GS reference mapper from 454, and usually when I used the SNP.txt files there was no problem. Now I receive an error " unable to parse known SNPs file" both for 141 and for 142.

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Dina Volodarsky-Baum, M.Sc
DYN Labs. Ltd.
P.O.B. 3063
7 Ha'Eshel st.
Caesarea Industrial Park 38900 Israel

Mobile:    +972-52-7715358
e-mail: di...@dyn.co.il

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Dina Volodarsky-Baum, M.Sc
DYN Labs. Ltd.
P.O.B. 3063
7 Ha'Eshel st.
Caesarea Industrial Park 38900 Israel

Mobile:    +972-52-7715358
e-mail: di...@dyn.co.il