ERROR: Variant physical position must be monotonically increasing.

[Tom159357]

 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:
   
   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]

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 :

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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.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. — Reply to this email directly, view it on GitHub <#128>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABAKRQUB3DGE6FYIT23HFJLZ2TH53AVCNFSM6AAAAABPTZ6LLCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU3TIOJYGA4DCMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>