szpiech
commented
4 months ago Hello,
Yes I believe the reason you don’t get any output is because all your genetic distances are equal. It is an oversight that selscan is allowed to function this way without errors or warnings.
When you use —pmap (and provide vcf files) you don’t need to provide any map file (—pmap is a true/false flag). With —pmap set, selscan will take the physical distance information from the vcf file.
Hope this helps,
Zachary
Le ven. 17 mai 2024 à 10:16, Tom159357 @.***> a écrit :
Dear Szpiech Hello,I encountered some issues when using selscan to calculate XP-EHH。 ①I don't quite understand the map file.My map file is generated like this：vcftools --vcf SNP_merge.vcf --plink --out SNP.The generated file is：1 1:146 0 146.My command is：./selscan --xpehh --vcf --vcf-ref --map --out .The third column of the map file is all 0, running without any errors, but the output. xpeh.out is empty,is this because the genetic distance of the. map file is all 0? Why is the third column set to 0 and this command still running, but the. xpeh. out file is empty and the. xpeh. log only has partial bit information (WANING: Reached chrome edge before EHH retired below 0.05 Skipping calculation at position 146 id: 1:146)? ）②--pmap : Use physical map instead of a genetic map.What is the format of the pmap file, what is it generated from, and how many columns of information are there.I want to use pmap instead of map.When I use: selscan -- xpehh -- vcf-- vcf ref-- pmap-- out, an error will be reported: ERROR: command line flag chr2pmap.map not recognized Thank you very much!Looking forward to your reply.
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Dear Szpiech Hello,I encountered some issues when using selscan to calculate XP-EHH。 ①I don't quite understand the map file.My map file is generated like this：vcftools --vcf SNP_merge.vcf --plink --out SNP.The generated file is：1 1:146 0 146.My command is：./selscan --xpehh --vcf --vcf-ref --map --out .The third column of the map file is all 0, running without any errors, but the output. xpeh.out is empty,is this because the genetic distance of the. map file is all 0? Why is the third column set to 0 and this command still running, but the. xpeh. out file is empty and the. xpeh. log only has partial bit information (WANING: Reached chrome edge before EHH retired below 0.05 Skipping calculation at position 146 id: 1:146)?
）②--pmap : Use physical map instead of a genetic map.What is the format of the pmap file, what is it generated from, and how many columns of information are there.I want to use pmap instead of map.When I use: selscan -- xpehh -- vcf-- vcf ref-- pmap-- out, an error will be reported: ERROR: command line flag chr2pmap.map not recognized
Thank you very much!Looking forward to your reply.