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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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Disagreement between wiki and actual usage for ascatSnpPanelMerge #93

Open cboursnell opened 4 years ago

cboursnell commented 4 years ago

On the wiki https://github.com/cancerit/ascatNgs/wiki/Reference-files-from-normal-sample-data it says you can run ascatSnpPanelMerge like this:

ascatSnpPanelMerge.pl genome.fa sampleA-hets.tsv.0 [sampleB-hets.tsv.0] > SnpPositions.tsv

where you increment the names of the samples, but keep the .0 as the suffix. When trying this I got the error from the script saying Can't use an undefined value as an ARRAY reference at /opt/wtsi-cgp/bin/ascatSnpPanelMerge.pl line 55.

If I rename my inputs to sample.tsv.0, sample.tsv.1 ... etc then the script runs fine and produces expected output. The method described in the wiki seems better to me.

rulixxx commented 4 years ago

Hi Chris!

Have been recently using this piece of code myself. I think that you got it correctly the first time. One increments the sample names but keeps the numeric suffix constant.

Looking trough the code it seems that the suffix is one based and not zero based as the wiki seems to suggest. I think that is what is causing your error

panxiaoguang commented 1 year ago

how many memories you use for the scripts? only one file need more than 200G?