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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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-X option does not work #27

Closed ymatmt closed 3 years ago

ymatmt commented 3 years ago

Hi,

I want to remove telomere regions in the genome so I run raisd using -X option with tab txt as follows,

RAiSD -n vcf_run -t -f -P -R -s -A 0.995 -X remove.txt -I ${VFILE}

cat remove.txt A1 0 100000 A1 243404654 243504654 X 0 100000 X 129529249 129629249

However I obtained same file as one without '-X' option, i.e. the result contained all region including above the regions. How can I fix this?

Thank you.

alachins commented 3 years ago

Hi, Everything seems correct in the remove.txt file. If you could send me the files to reproduce this, I will check what is happening there. Best regards, Nikos A.

On Wed, Jun 23, 2021 at 10:43 AM ymatmt @.***> wrote:

Hi,

I want to remove telomere regions in the genome so I run raisd using -X option with tab txt as follows,

RAiSD -n vcf_run -t -f -P -R -s -A 0.995 -X remove.txt -I ${VFILE}

cat remove.txt A1 0 100000 A1 243404654 243504654 X 0 100000 X 129529249 129629249

However I obtained same file as one without '-X' option, i.e. the result contained all region including above the regions. How can I fix this?

Thank you.

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ymatmt commented 3 years ago

Hi,

Thank you for your kind comments. I confirm the chromosome number of VCF file then the chromosome character in VCF file is different from it in the remove file. So I revise the remove file then the problem is fixed! I am so sorry bothering you.

Thank you!