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mcfrith / tandem-genotypes

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Error when using -g refGene.txt option #10

Closed MeiShu00 closed 3 years ago

MeiShu00 commented 3 years ago

Hi,

When i ran the following command tandem-genotypes -g refGene.txt microstat.txt input.maf > output.txt, i encountered the following error:

image

Hence, i would like to clarify the following questions:

  1. I understand that it is ok to omit -g refGene.txt and i was able to get an output.txt file via this method. However, i would like to check if omitting the refgene.txt file would affect the output text file.

  2. As my reads are aligned using hg38 , i would also like to check if downloading the refGene table from UCSC table browser (https://genome-euro.ucsc.edu/cgi-bin/hgTables?hgsid=262439517_q2No2a0kysSpzsTA6blcVDh4e3nM&clade=mammal&org=Human&db=hg38&hgta_group=allTables&hgta_track=hg38&hgta_table=refGene&hgta_regionType=range&position=chr4%3A3%2C379%2C000-3%2C379%2C046&hgta_outputType=primaryTable&hgta_outFileName=SNP_loc_chr4%3A3379000-3379046.txt) is the same as the refGene.txt file that was mentioned in the README.md. I also got my microsat.txt file from the same source.

Thank you :D

mcfrith commented 3 years ago

Thanks for reporting this problem, which helps to improve tandem-genotypes! It should be fixed in the newest version 1.8.2 (but I'm not sure when it will get into bioconda).

(The problem was that it didn't like the 1st line starting with "#" in your refGene.txt.)

If you omit -g refGene.txt, I think it only changes the gene annotations, and the order of the output lines (which are ordered by "importance").

If you download the table from there, I think it's the same (apart from the 1st line starting with "#"!)