Newbie stuck with Galaxy filter

[kcarss]

Hi

I have a question about the filter function of Galaxy. I am new to NGS data analysis, and am not a bioinformatician!

I am trying to identify SNPs from a large dataset (pileup format) amassed from 1000genomes data. I have filtered according to quality (20) and coverage (6), and checked the ‘variants only’ box, which gives me a dataset of 3.7 million lines.

This dataset seems to include all lines where at least one of the reads specifies a variant, even if it is only 1 out of 6 or more reads, and even when the consensus base is the same as the reference. Therefore I have been trying to filter the dataset again using the filter function, to identify only those lines where the consensus base differs from the reference. This is where I am getting stuck.

I have tried several things inc both filter and filter on ambiguities; using spaces vs no spaces in the expression; == vs != etc but I always get an error message something like:

empty, format: interval, database: hg18
Info: Filtering with c4==c5,
kept 0.00% of 3680832 lines.
Skipped 3680830 invalid lines starting at line #1: "chr10 52984 52985 C C 30 0 12 6 T,..,, @ACCCA !-!!08 0 5 0 1 6"

I can’t figure out what I am doing wrong!

Any help would be greatly appreciated.

[culmen]

Hi Kcarss,

I am also stuck up with same kind of problem. Have you solved that? If so can please let me know the trick.
As you mentioned,

Amassed large dataset from 1000genomes data

Have you downloaded the entire data from 1000genomes ftp? I find some computing problems in downloading too?

Thanks a lot,
Culmen

[kcarss]

Hi Culmen

I never did solve that problem I'm afraid.

I downloaded all of the 1000genomes sequencing data of one individual from pilot 2.

K