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szpiech / selscan

Haplotype based scans for selection
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ERROR: Variant physical position must be monotonically increasing. #128

Open Tom159357 opened 1 month ago

Tom159357 commented 1 month ago 
 Dear author, hello. I encountered an issue while running selscan: ERROR: Variant physical position must be monotonically increasing.2__34 34 appears after 1__230155 230155
 My processing procedure is:
  1. Remove the./. from the vcf file: vcftools --vcf "$vcf_file" --max-missing 1.0 --recode --stdout > No_missing.vcf
  2. Obtain vcf files of different lineage strains from the total vcf file： bcftools view -S $list1 $input_vcf -o 1_domestic.vcf bcftools view -S $list2 $input_vcf -o 1_ref.vcf
  3. Run selscan,: $selscan -- xpehh -- vcf $vcf_domestic -- vcf ref $vcf_ref -- pmap -- out --threads 2 The output result will report an error: a49768d575467e72aa07f4d2af48532f When running selscan, is it necessary to split both vcf files into one sub vcf file with only one chromosome, and then perform two selscans? I am looking forward to your reply.
szpiech commented 1 month ago

Hello,

You will need to split your files by chromosome and run them separately. You can then jointly normalize with the norm program.

Hope this helps,

Zachary

Le mer. 9 oct. 2024 à 02:59, Tom159357 @.***> a écrit :

Dear author, hello. I encountered an issue while running selscan: ERROR: Variant physical position must be monotonically increasing.234 34 appears after 1230155 230155 My processing procedure is:

  1. Remove the./. from the vcf file: vcftools --vcf "$vcf_file" --max-missing 1.0 --recode --stdout > No_missing.vcf
  2. Obtain vcf files of different lineage strains from the total vcf file： bcftools view -S $list1 $input_vcf -o 1_domestic.vcf bcftools view -S $list2 $input_vcf -o 1_ref.vcf
  3. Run selscan,: $selscan -- xpehh -- vcf $vcf_domestic -- vcf ref $vcf_ref -- pmap -- out --threads 2 The output result will report an error: a49768d575467e72aa07f4d2af48532f.png (view on web) https://github.com/user-attachments/assets/38ec30b3-e6df-4ea7-91cb-00fc7a7ea6bb When running selscan, is it necessary to split both vcf files into one sub vcf file with only one chromosome, and then perform two selscans? I am looking forward to your reply.

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